diff --git a/dev/integration_tests/data_asset_app/hook/build.dart b/dev/integration_tests/data_asset_app/hook/build.dart
index 25aa7480d17ed..2c92a7e54dff8 100644
--- a/dev/integration_tests/data_asset_app/hook/build.dart
+++ b/dev/integration_tests/data_asset_app/hook/build.dart
@@ -17,6 +17,7 @@ void main(List<String> args) async {
             file: input.packageRoot.resolve('data/$id'),
           ),
         );
+        output.dependencies.add(input.packageRoot.resolve('data/$id'));
       }
     }
   });
diff --git a/dev/integration_tests/data_asset_app/pubspec.yaml b/dev/integration_tests/data_asset_app/pubspec.yaml
index 905d6be746144..a05bb29bd5e94 100644
--- a/dev/integration_tests/data_asset_app/pubspec.yaml
+++ b/dev/integration_tests/data_asset_app/pubspec.yaml
@@ -12,8 +12,8 @@ resolution: workspace
 dependencies:
   flutter:
     sdk: flutter
-  hooks: ^1.0.2
-  data_assets: ^0.19.6
+  hooks: ^2.0.0
+  data_assets: ^0.20.0
   data_asset_package:
     path: ../data_asset_package
 
@@ -24,4 +24,4 @@ dev_dependencies:
 flutter:
   uses-material-design: true
 
-# PUBSPEC CHECKSUM: jl85h
+# PUBSPEC CHECKSUM: 9jmf6j
diff --git a/dev/integration_tests/data_asset_package/.gitignore b/dev/integration_tests/data_asset_package/.gitignore
index dd5eb98951f29..f966f4da52b56 100644
--- a/dev/integration_tests/data_asset_package/.gitignore
+++ b/dev/integration_tests/data_asset_package/.gitignore
@@ -29,3 +29,6 @@ migrate_working_dir/
 .flutter-plugins-dependencies
 /build/
 /coverage/
+
+# Generated test file.
+data/generated.txt
diff --git a/dev/integration_tests/data_asset_package/hook/build.dart b/dev/integration_tests/data_asset_package/hook/build.dart
index 25aa7480d17ed..bc16610c7cd90 100644
--- a/dev/integration_tests/data_asset_package/hook/build.dart
+++ b/dev/integration_tests/data_asset_package/hook/build.dart
@@ -2,6 +2,8 @@
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 
+import 'dart:io';
+
 import 'package:data_assets/data_assets.dart';
 import 'package:hooks/hooks.dart';
 
@@ -17,7 +19,28 @@ void main(List<String> args) async {
             file: input.packageRoot.resolve('data/$id'),
           ),
         );
+        // If the file is modified, the hook needs to be rerun. (Technically, we
+        // don't need to rerun because we'd output the exact same thing. But the
+        // hook could be doing other things based on the input file.)
+        output.dependencies.add(input.packageRoot.resolve('data/$id'));
+      }
+
+      // Generate a data asset in the hook.
+      // It is better to generate to outputDirectoryShared, but users might do
+      // this instead and then delete the file manually.
+      final Uri generatedUri = input.packageRoot.resolve('data/generated.txt');
+      final file = File(generatedUri.toFilePath());
+      if (!file.parent.existsSync()) {
+        file.parent.createSync(recursive: true);
       }
+      file.writeAsStringSync('generated content');
+      output.assets.data.add(
+        DataAsset(
+          package: input.packageName,
+          name: 'data/generated.txt',
+          file: generatedUri,
+        ),
+      );
     }
   });
 }
diff --git a/dev/integration_tests/data_asset_package/pubspec.yaml b/dev/integration_tests/data_asset_package/pubspec.yaml
index 2fa645acffd85..9e4421c759c07 100644
--- a/dev/integration_tests/data_asset_package/pubspec.yaml
+++ b/dev/integration_tests/data_asset_package/pubspec.yaml
@@ -12,8 +12,8 @@ resolution: workspace
 dependencies:
   flutter:
     sdk: flutter
-  hooks: ^1.0.2
-  data_assets: ^0.19.6
+  hooks: ^2.0.0
+  data_assets: ^0.20.0
 
 dev_dependencies:
   flutter_test:
@@ -22,4 +22,4 @@ dev_dependencies:
 flutter:
   uses-material-design: true
 
-# PUBSPEC CHECKSUM: 2g5j7i
+# PUBSPEC CHECKSUM: 6cfeb0
diff --git a/dev/integration_tests/hook_user_defines/pubspec.yaml b/dev/integration_tests/hook_user_defines/pubspec.yaml
index 2e4a3869b7740..b620a7dc63e14 100644
--- a/dev/integration_tests/hook_user_defines/pubspec.yaml
+++ b/dev/integration_tests/hook_user_defines/pubspec.yaml
@@ -15,11 +15,11 @@ hooks:
       magic_value: 1000
 
 dependencies:
-  hooks: 1.0.3
+  hooks: 2.0.0
   logging: 1.3.0
-  native_toolchain_c: 0.17.6
+  native_toolchain_c: 0.19.0
 
 dev_dependencies:
   test: 1.29.0
 
-# PUBSPEC CHECKSUM: 30ohqf
+# PUBSPEC CHECKSUM: jmsrr2
diff --git a/dev/integration_tests/record_use_test_package/pubspec.yaml b/dev/integration_tests/record_use_test_package/pubspec.yaml
index 1248355fba1c9..d1d6efbe2e9fc 100644
--- a/dev/integration_tests/record_use_test_package/pubspec.yaml
+++ b/dev/integration_tests/record_use_test_package/pubspec.yaml
@@ -11,8 +11,8 @@ environment:
 dependencies:
   flutter:
     sdk: flutter
-  hooks: ^1.0.2
-  data_assets: ^0.19.6
+  hooks: ^2.0.0
+  data_assets: ^0.20.0
   record_use: 0.6.0
   meta: 1.18.2
 
@@ -23,4 +23,4 @@ dev_dependencies:
 flutter:
   uses-material-design: true
 
-# PUBSPEC CHECKSUM: 4e6oin
+# PUBSPEC CHECKSUM: gl7kb7
diff --git a/packages/flutter_tools/lib/src/build_system/targets/hook_runner_native.dart b/packages/flutter_tools/lib/src/build_system/targets/hook_runner_native.dart
index e3e835b7b89f3..eb8c192dd453b 100644
--- a/packages/flutter_tools/lib/src/build_system/targets/hook_runner_native.dart
+++ b/packages/flutter_tools/lib/src/build_system/targets/hook_runner_native.dart
@@ -37,7 +37,7 @@ class FlutterHookRunnerNative implements FlutterHookRunner {
       environment,
     );
 
-    final DartHooksResult dartHooksResult = await runFlutterSpecificHooks(
+    final (:DartHooksResult buildResult, results: _) = await runFlutterSpecificBuildHooks(
       environmentDefines: environment.defines,
       buildRunner: buildRunner,
       targetPlatform: targetPlatform,
@@ -45,10 +45,9 @@ class FlutterHookRunnerNative implements FlutterHookRunner {
       fileSystem: environment.fileSystem,
       buildCodeAssets: null,
       buildDataAssets: true,
-      recordedUsesFile: null,
     );
 
-    final FlutterHookResult flutterHookResult = dartHooksResult.asFlutterResult;
+    final FlutterHookResult flutterHookResult = buildResult.asFlutterResult;
     _flutterHookResult = flutterHookResult;
     logger?.printTrace('runHooks() - done');
     return flutterHookResult;
diff --git a/packages/flutter_tools/lib/src/build_system/targets/native_assets.dart b/packages/flutter_tools/lib/src/build_system/targets/native_assets.dart
index 40aacae6c3973..3a3fb42e3190b 100644
--- a/packages/flutter_tools/lib/src/build_system/targets/native_assets.dart
+++ b/packages/flutter_tools/lib/src/build_system/targets/native_assets.dart
@@ -57,8 +57,8 @@ class BuildHooks extends Target {
     final FlutterNativeAssetsBuildRunner buildRunner =
         _buildRunner ?? await createFlutterNativeAssetsBuildRunner(environment);
     final (
-      results: SerializedBuildResults results,
-      dependencies: List<Uri> dependencies,
+      :SerializedBuildResults results,
+      :DartHooksResult buildResult,
     ) = await runFlutterSpecificBuildHooks(
       environmentDefines: environment.defines,
       buildRunner: buildRunner,
@@ -74,11 +74,20 @@ class BuildHooks extends Target {
       dartBuildOutputJsonFile.parent.createSync(recursive: true);
     }
 
-    dartBuildOutputJsonFile.writeAsStringSync(json.encode(results));
+    final String encodedResults = json.encode(results);
+    if (!dartBuildOutputJsonFile.existsSync() ||
+        dartBuildOutputJsonFile.readAsStringSync() != encodedResults) {
+      dartBuildOutputJsonFile.writeAsStringSync(encodedResults);
+    }
 
+    final Set<Uri> buildDependencies = buildResult.dependencies.toSet();
     final depfile = Depfile(
-      <File>[for (final Uri dependency in dependencies) fileSystem.file(dependency)],
-      <File>[fileSystem.file(dartBuildOutputJsonFile)],
+      <File>[for (final Uri dependency in buildResult.dependencies) fileSystem.file(dependency)],
+      <File>[
+        fileSystem.file(dartBuildOutputJsonFile),
+        for (final Uri uri in buildResult.filesToBeBundled)
+          if (!buildDependencies.contains(uri)) fileSystem.file(uri),
+      ],
     );
     final File outputDepfile = environment.buildDir.childFile(depFilename);
     if (!outputDepfile.parent.existsSync()) {
@@ -98,7 +107,6 @@ class BuildHooks extends Target {
     // If different packages are resolved, different native assets might need to
     // be built.
     Source.pattern('{WORKSPACE_DIR}/.dart_tool/package_config.json'),
-    // TODO(mosuem): Should consume resources.json. https://github.com/flutter/flutter/issues/146263
   ];
 
   @override
@@ -197,6 +205,8 @@ class LinkHooks extends Target {
     final buildMode = BuildMode.fromCliName(buildModeEnvironment);
     final File? recordedUsesFileToPass = getRecordedUsesFile(environment, buildMode);
 
+    final linkingEnabled = buildMode != BuildMode.debug;
+
     // Read the result of BuildHooks.
     final File dartBuildOutputJsonFile = environment.buildDir.childFile(BuildHooks.resultFilename);
     if (!dartBuildOutputJsonFile.existsSync()) {
@@ -207,29 +217,52 @@ class LinkHooks extends Target {
     final Map<String, Map<String, Object?>> buildResults = serializedBuildResults
         .cast<String, Map<String, Object?>>();
 
-    final DartHooksResult result = await runFlutterSpecificLinkHooks(
+    final DartHooksResult linkResult;
+    if (linkingEnabled) {
+      linkResult = await runFlutterSpecificLinkHooks(
+        environmentDefines: environment.defines,
+        buildRunner: buildRunner,
+        targetPlatform: targetPlatform,
+        projectUri: projectUri,
+        fileSystem: fileSystem,
+        buildCodeAssets: BuildCodeAssetsOptions(appBuildDirectory: environment.outputDir),
+        buildDataAssets: true,
+        buildResults: buildResults,
+        recordedUsesFile: recordedUsesFileToPass,
+      );
+    } else {
+      linkResult = DartHooksResult.empty();
+    }
+
+    final DartHooksResult combinedResult = combineBuildAndLinkResults(
       environmentDefines: environment.defines,
-      buildRunner: buildRunner,
       targetPlatform: targetPlatform,
-      projectUri: projectUri,
       fileSystem: fileSystem,
       buildCodeAssets: BuildCodeAssetsOptions(appBuildDirectory: environment.outputDir),
       buildDataAssets: true,
       buildResults: buildResults,
-      recordedUsesFile: recordedUsesFileToPass,
+      linkResult: linkResult,
     );
 
     final File dartHookResultJsonFile = environment.buildDir.childFile(resultFilename);
     if (!dartHookResultJsonFile.parent.existsSync()) {
       dartHookResultJsonFile.parent.createSync(recursive: true);
     }
-    dartHookResultJsonFile.writeAsStringSync(json.encode(result.toJson()));
-
+    // TODO(dcharkes): The build system uses file hashing to determine if
+    // targets need to be rerun. Because combinedResult.toJson() includes
+    // transient build_start and build_end times, this file is rewritten on
+    // every build causing downstream targets to rerun. We should remove
+    // build_start and build_end from the JSON representation entirely in a
+    // future PR.
+    dartHookResultJsonFile.writeAsStringSync(json.encode(combinedResult.toJson()));
+    final Set<Uri> linkDependencies = linkResult.dependencies.toSet();
     final depfile = Depfile(
-      <File>[for (final Uri dependency in result.dependencies) fileSystem.file(dependency)],
+      <File>[for (final Uri dependency in linkResult.dependencies) fileSystem.file(dependency)],
       <File>[
         fileSystem.file(dartHookResultJsonFile),
-        for (final Uri uri in result.filesToBeBundled) fileSystem.file(uri),
+        if (linkingEnabled)
+          for (final Uri uri in linkResult.filesToBeBundled)
+            if (!linkDependencies.contains(uri)) fileSystem.file(uri),
       ],
     );
     final File outputDepfile = environment.buildDir.childFile(depFilename);
@@ -278,8 +311,8 @@ class InstallCodeAssets extends Target {
     final FileSystem fileSystem = environment.fileSystem;
     final TargetPlatform targetPlatform = _getTargetPlatformFromEnvironment(environment, name);
 
-    // We fetch the result from the [LinkHooks].
-    final DartHooksResult dartHookResult = await LinkHooks.loadHookResult(environment);
+    // We fetch the combined result from the [LinkHooks].
+    final DartHooksResult combinedResult = await LinkHooks.loadHookResult(environment);
 
     // And install/copy the code assets to the right place and create a
     // native_asset.yaml that can be used by the final AOT compilation.
@@ -293,7 +326,7 @@ class InstallCodeAssets extends Target {
     }
 
     final List<File> installedFiles = await installCodeAssets(
-      dartHookResult: dartHookResult,
+      dartHookResult: combinedResult,
       environmentDefines: environment.defines,
       targetPlatform: targetPlatform,
       projectUri: projectUri,
@@ -304,7 +337,7 @@ class InstallCodeAssets extends Target {
     assert(fileSystem.file(nativeAssetsFileUri).existsSync());
 
     final depfile = Depfile(<File>[
-      for (final Uri file in dartHookResult.filesToBeBundled) fileSystem.file(file),
+      for (final Uri file in combinedResult.filesToBeBundled) fileSystem.file(file),
     ], installedFiles);
     final File outputDepfile = environment.buildDir.childFile(depFilename);
     environment.depFileService.writeToFile(depfile, outputDepfile);
diff --git a/packages/flutter_tools/lib/src/isolated/native_assets/native_assets.dart b/packages/flutter_tools/lib/src/isolated/native_assets/native_assets.dart
index ab02077c618f9..3e0ec38639659 100644
--- a/packages/flutter_tools/lib/src/isolated/native_assets/native_assets.dart
+++ b/packages/flutter_tools/lib/src/isolated/native_assets/native_assets.dart
@@ -87,10 +87,7 @@ Future<DartHooksResult> runFlutterSpecificHooks({
 
   final buildStart = DateTime.now();
 
-  final (
-    results: SerializedBuildResults results,
-    dependencies: List<Uri> dependencies,
-  ) = await runFlutterSpecificBuildHooks(
+  final (:SerializedBuildResults results, buildResult: _) = await runFlutterSpecificBuildHooks(
     environmentDefines: environmentDefines,
     buildRunner: buildRunner,
     targetPlatform: targetPlatform,
@@ -100,24 +97,44 @@ Future<DartHooksResult> runFlutterSpecificHooks({
     buildDataAssets: buildDataAssets,
   );
 
-  final DartHooksResult linkResult = await runFlutterSpecificLinkHooks(
+  final BuildMode buildMode = _getBuildMode(
+    environmentDefines,
+    targetPlatform == TargetPlatform.tester,
+  );
+  final bool linkingEnabled = _nativeAssetsLinkingEnabled(buildMode);
+  final DartHooksResult linkResult;
+  if (linkingEnabled) {
+    linkResult = await runFlutterSpecificLinkHooks(
+      environmentDefines: environmentDefines,
+      buildRunner: buildRunner,
+      targetPlatform: targetPlatform,
+      projectUri: projectUri,
+      fileSystem: fileSystem,
+      buildCodeAssets: buildCodeAssets,
+      buildDataAssets: buildDataAssets,
+      buildResults: results,
+      recordedUsesFile: recordedUsesFile,
+    );
+  } else {
+    linkResult = DartHooksResult.empty();
+  }
+
+  final DartHooksResult combinedResult = combineBuildAndLinkResults(
     environmentDefines: environmentDefines,
-    buildRunner: buildRunner,
     targetPlatform: targetPlatform,
-    projectUri: projectUri,
     fileSystem: fileSystem,
     buildCodeAssets: buildCodeAssets,
     buildDataAssets: buildDataAssets,
     buildResults: results,
-    recordedUsesFile: recordedUsesFile,
+    linkResult: linkResult,
   );
 
   return DartHooksResult(
     buildStart: buildStart,
-    buildEnd: linkResult.buildEnd,
-    codeAssets: linkResult.codeAssets,
-    dataAssets: linkResult.dataAssets,
-    dependencies: <Uri>{...dependencies, ...linkResult.dependencies}.toList(),
+    buildEnd: combinedResult.buildEnd,
+    codeAssets: combinedResult.codeAssets,
+    dataAssets: combinedResult.dataAssets,
+    dependencies: combinedResult.dependencies,
   );
 }
 
@@ -125,7 +142,8 @@ Future<DartHooksResult> runFlutterSpecificHooks({
 ///
 /// Returns the serialized build results per target and the list of dependencies
 /// collected during the build stage.
-Future<({SerializedBuildResults results, List<Uri> dependencies})> runFlutterSpecificBuildHooks({
+Future<({SerializedBuildResults results, DartHooksResult buildResult})>
+runFlutterSpecificBuildHooks({
   required Map<String, String> environmentDefines,
   required FlutterNativeAssetsBuildRunner buildRunner,
   required TargetPlatform targetPlatform,
@@ -135,9 +153,11 @@ Future<({SerializedBuildResults results, List<Uri> dependencies})> runFlutterSpe
   required bool buildDataAssets,
 }) async {
   if (!await _hookRunRequired(buildRunner)) {
-    return (results: const <String, Map<String, Object?>>{}, dependencies: const <Uri>[]);
+    return (results: const <String, Map<String, Object?>>{}, buildResult: DartHooksResult.empty());
   }
 
+  final buildStart = DateTime.now();
+
   final (
     targets: List<AssetBuildTarget> targets,
     buildMode: BuildMode buildMode,
@@ -158,6 +178,9 @@ Future<({SerializedBuildResults results, List<Uri> dependencies})> runFlutterSpe
 
   final results = <String, Map<String, Object?>>{};
   final dependencies = <Uri>{};
+  final codeAssets = <FlutterCodeAsset>[];
+  final dataAssets = <DataAsset>[];
+
   for (var i = 0; i < targets.length; i++) {
     final AssetBuildTarget target = targets[i];
     // Only run non-code extensions (like data assets) for the first target,
@@ -168,9 +191,25 @@ Future<({SerializedBuildResults results, List<Uri> dependencies})> runFlutterSpe
     final BuildResult buildResult = await _build(buildRunner, extensions, linkingEnabled);
     results[target.targetString] = buildResult.toJson();
     dependencies.addAll(buildResult.dependencies);
+    _decodeAssets(
+      encodedAssets: buildResult.encodedAssets,
+      target: target,
+      codeAssetsAccumulator: codeAssets,
+      dataAssetsAccumulator: dataAssets,
+    );
   }
+  _checkForDuplicateAssets(codeAssets: codeAssets, dataAssets: dataAssets, targets: targets);
   globals.logger.printTrace('Running build hooks for $targetString done.');
-  return (results: results, dependencies: dependencies.toList());
+  return (
+    results: results,
+    buildResult: DartHooksResult(
+      buildStart: buildStart,
+      buildEnd: DateTime.now(),
+      codeAssets: codeAssets,
+      dataAssets: dataAssets,
+      dependencies: dependencies.toList(),
+    ),
+  );
 }
 
 List<AssetBuildTarget> _getTargets({
@@ -241,11 +280,8 @@ Future<({List<AssetBuildTarget> targets, BuildMode buildMode, bool linkingEnable
 
 /// Invokes the link hooks of all transitive Dart package hooks.
 ///
-/// It takes the [buildResults] produced by [runFlutterSpecificBuildHooks] and
-/// returns a [DartHooksResult] containing the aggregated assets from both the
-/// build results and the link hooks.
-///
 /// The returned dependencies only include those collected during the link stage.
+/// The returned assets only include those produced during the link stage.
 Future<DartHooksResult> runFlutterSpecificLinkHooks({
   required Map<String, String> environmentDefines,
   required FlutterNativeAssetsBuildRunner buildRunner,
@@ -297,54 +333,25 @@ Future<DartHooksResult> runFlutterSpecificLinkHooks({
     }
     final buildResult = BuildResult.fromJson(buildResultJson);
 
-    LinkResult? linkResult;
     if (linkingEnabled) {
-      linkResult = await _link(buildRunner, extensions, buildResult, recordedUsesFile);
-
-      if (target is CodeAssetTarget) {
-        codeAssets
-          ..addAll(
-            _filterCodeAssets(
-              linkResult.encodedAssets,
-              Target.fromArchitectureAndOS(target.architecture, target.os),
-            ),
-          )
-          ..addAll(
-            _filterCodeAssets(
-              buildResult.encodedAssets,
-              Target.fromArchitectureAndOS(target.architecture, target.os),
-            ),
-          );
-      }
-      dataAssets
-        ..addAll(_filterDataAssets(linkResult.encodedAssets))
-        ..addAll(_filterDataAssets(buildResult.encodedAssets));
+      final LinkResult linkResult = await _link(
+        buildRunner,
+        extensions,
+        buildResult,
+        recordedUsesFile,
+      );
+
+      _decodeAssets(
+        encodedAssets: linkResult.encodedAssets,
+        target: target,
+        codeAssetsAccumulator: codeAssets,
+        dataAssetsAccumulator: dataAssets,
+      );
       dependencies.addAll(linkResult.dependencies);
-    } else {
-      if (target is CodeAssetTarget) {
-        codeAssets.addAll(
-          _filterCodeAssets(
-            buildResult.encodedAssets,
-            Target.fromArchitectureAndOS(target.architecture, target.os),
-          ),
-        );
-      }
-      dataAssets.addAll(_filterDataAssets(buildResult.encodedAssets));
-      dependencies.addAll(buildResult.dependencies);
     }
   }
 
-  if (dataAssets.map((DataAsset asset) => asset.id).toSet().length != dataAssets.length) {
-    throwToolExit(
-      'Found duplicates in the data assets: ${dataAssets.map((DataAsset e) => e.id).toList()} while compiling for ${targets.map((AssetBuildTarget e) => e.targetString).toList()}.',
-    );
-  }
-
-  if (codeAssets.toSet().length != codeAssets.length) {
-    throwToolExit(
-      'Found duplicates in the code assets: ${codeAssets.map((FlutterCodeAsset e) => e.codeAsset.id).toList()} while compiling for ${targets.map((AssetBuildTarget e) => e.targetString).toList()}.',
-    );
-  }
+  _checkForDuplicateAssets(codeAssets: codeAssets, dataAssets: dataAssets, targets: targets);
 
   globals.logger.printTrace('Running link hooks for $targetString done.');
 
@@ -357,6 +364,117 @@ Future<DartHooksResult> runFlutterSpecificLinkHooks({
   );
 }
 
+/// Combines build-stage and link-stage results into a single, combined [DartHooksResult].
+///
+/// The combined result contains all code and data assets from both stages,
+/// and the union of all dependencies from both stages.
+DartHooksResult combineBuildAndLinkResults({
+  required Map<String, String> environmentDefines,
+  required TargetPlatform targetPlatform,
+  required FileSystem fileSystem,
+  required BuildCodeAssetsOptions? buildCodeAssets,
+  required bool buildDataAssets,
+  required SerializedBuildResults buildResults,
+  required DartHooksResult linkResult,
+}) {
+  final List<AssetBuildTarget> targets = _getTargets(
+    environmentDefines: environmentDefines,
+    targetPlatform: targetPlatform,
+    fileSystem: fileSystem,
+    buildCodeAssets: buildCodeAssets,
+    buildDataAssets: buildDataAssets,
+  );
+
+  final codeAssets = <FlutterCodeAsset>[...linkResult.codeAssets];
+  final dataAssets = <DataAsset>[...linkResult.dataAssets];
+  final dependencies = <Uri>{...linkResult.dependencies};
+
+  for (final target in targets) {
+    final Map<String, Object?>? buildResultJson = buildResults[target.targetString];
+    if (buildResultJson == null) {
+      continue;
+    }
+    final buildResult = BuildResult.fromJson(buildResultJson);
+    _decodeAssets(
+      encodedAssets: buildResult.encodedAssets,
+      target: target,
+      codeAssetsAccumulator: codeAssets,
+      dataAssetsAccumulator: dataAssets,
+    );
+    dependencies.addAll(buildResult.dependencies);
+  }
+
+  _checkForDuplicateAssets(codeAssets: codeAssets, dataAssets: dataAssets, targets: targets);
+
+  return DartHooksResult(
+    buildStart: linkResult.buildStart,
+    buildEnd: linkResult.buildEnd,
+    codeAssets: codeAssets,
+    dataAssets: dataAssets,
+    dependencies: dependencies.toList(),
+  );
+}
+
+/// Extracts and categorizes code and data assets from [encodedAssets] for the given [target].
+///
+/// The extracted assets are appended to the optional accumulator lists:
+/// - [codeAssetsAccumulator]: Collects matching [FlutterCodeAsset]s.
+/// - [dataAssetsAccumulator]: Collects matching [DataAsset]s.
+void _decodeAssets({
+  required Iterable<EncodedAsset> encodedAssets,
+  required AssetBuildTarget target,
+  List<FlutterCodeAsset>? codeAssetsAccumulator,
+  List<DataAsset>? dataAssetsAccumulator,
+}) {
+  if (target is CodeAssetTarget) {
+    final Iterable<FlutterCodeAsset> filteredCode = _filterCodeAssets(
+      encodedAssets,
+      Target.fromArchitectureAndOS(target.architecture, target.os),
+    );
+    codeAssetsAccumulator?.addAll(filteredCode);
+  }
+  final Iterable<DataAsset> filteredData = _filterDataAssets(encodedAssets);
+  dataAssetsAccumulator?.addAll(filteredData);
+}
+
+void _checkForDuplicateAssets({
+  required List<FlutterCodeAsset> codeAssets,
+  required List<DataAsset> dataAssets,
+  required List<AssetBuildTarget> targets,
+}) {
+  final List<String> targetStrings = targets.map((AssetBuildTarget e) => e.targetString).toList();
+
+  final dataAssetIds = <String>{};
+  final duplicateDataAssetIds = <String>{};
+  for (final asset in dataAssets) {
+    if (!dataAssetIds.add(asset.id)) {
+      duplicateDataAssetIds.add(asset.id);
+    }
+  }
+  if (duplicateDataAssetIds.isNotEmpty) {
+    throwToolExit(
+      'Found duplicates in the data assets: '
+      '${duplicateDataAssetIds.toList()} while compiling for '
+      '$targetStrings.',
+    );
+  }
+
+  final codeAssetIds = <(String, Target)>{};
+  final duplicateCodeAssetIds = <String>{};
+  for (final asset in codeAssets) {
+    if (!codeAssetIds.add((asset.codeAsset.id, asset.target))) {
+      duplicateCodeAssetIds.add(asset.codeAsset.id);
+    }
+  }
+  if (duplicateCodeAssetIds.isNotEmpty) {
+    throwToolExit(
+      'Found duplicates in the code assets: '
+      '${duplicateCodeAssetIds.toList()} while compiling for '
+      '$targetStrings.',
+    );
+  }
+}
+
 Future<List<File>> installCodeAssets({
   required DartHooksResult dartHookResult,
   required Map<String, String> environmentDefines,
diff --git a/packages/flutter_tools/lib/src/update_packages_pins.dart b/packages/flutter_tools/lib/src/update_packages_pins.dart
index 7be7f8d7890ac..19fe93ac62ae3 100644
--- a/packages/flutter_tools/lib/src/update_packages_pins.dart
+++ b/packages/flutter_tools/lib/src/update_packages_pins.dart
@@ -24,7 +24,7 @@ const kManuallyPinnedDependencies = <String, String>{
   'flutter_gallery_assets': '1.0.2', // Tests depend on the exact version.
   'flutter_template_images': '5.0.0', // Must always exactly match flutter_tools template.
   'material_color_utilities': '0.13.0', // Keep pinned to latest until 1.0.0.
-  'data_assets': '0.19.6', //  Keep pinned to latest until 1.0.0. Rolled by @dcharkes.
+  'data_assets': '0.20.0', //  Keep pinned to latest until 1.0.0. Rolled by @dcharkes.
   'record_use': '0.6.0', //  Keep pinned to latest until 1.0.0. Rolled by @dcharkes.
 };
 
diff --git a/packages/flutter_tools/pubspec.yaml b/packages/flutter_tools/pubspec.yaml
index 4fdf0966f974e..475cee3f06341 100644
--- a/packages/flutter_tools/pubspec.yaml
+++ b/packages/flutter_tools/pubspec.yaml
@@ -57,10 +57,10 @@ dependencies:
   pubspec_parse: 1.5.0
 
   graphs: 2.3.2
-  hooks_runner: 1.2.1
-  hooks: 1.0.3
-  code_assets: 1.0.0
-  data_assets: 0.19.6
+  hooks_runner: 1.3.0
+  hooks: 2.0.0
+  code_assets: 1.1.0
+  data_assets: 0.20.0
 
   # We depend on very specific internal implementation details of the
   # 'test' package, which change between versions, so when upgrading
@@ -127,4 +127,4 @@ dartdoc:
   # Exclude this package from the hosted API docs.
   nodoc: true
 
-# PUBSPEC CHECKSUM: npmtr8
+# PUBSPEC CHECKSUM: vdpt2u
diff --git a/packages/flutter_tools/templates/package_ffi/pubspec.yaml.tmpl b/packages/flutter_tools/templates/package_ffi/pubspec.yaml.tmpl
index f9bb68dff1aa7..404f0e8844a0b 100644
--- a/packages/flutter_tools/templates/package_ffi/pubspec.yaml.tmpl
+++ b/packages/flutter_tools/templates/package_ffi/pubspec.yaml.tmpl
@@ -6,10 +6,10 @@ environment:
   sdk: {{dartSdkVersionBounds}}
 
 dependencies:
-  code_assets: ^1.0.0
-  hooks: ^1.0.0
+  code_assets: ^1.1.0
+  hooks: ^2.0.0
   logging: ^1.3.0
-  native_toolchain_c: ^0.17.4
+  native_toolchain_c: ^0.19.0
 
 dev_dependencies:
   ffi: ^2.1.4
diff --git a/packages/flutter_tools/test/general.shard/isolated/android/native_assets_test.dart b/packages/flutter_tools/test/general.shard/isolated/android/native_assets_test.dart
index 0b973fe35ef27..879276cddb958 100644
--- a/packages/flutter_tools/test/general.shard/isolated/android/native_assets_test.dart
+++ b/packages/flutter_tools/test/general.shard/isolated/android/native_assets_test.dart
@@ -78,8 +78,14 @@ void main() {
         ];
         final buildRunner = FakeFlutterNativeAssetsBuildRunner(
           packagesWithNativeAssetsResult: <String>['bar'],
-          buildResult: FakeFlutterNativeAssetsBuilderResult.fromAssets(codeAssets: codeAssets),
-          linkResult: FakeFlutterNativeAssetsBuilderResult.fromAssets(codeAssets: codeAssets),
+          buildResult: buildMode == BuildMode.debug
+              ? FakeFlutterNativeAssetsBuilderResult.fromAssets(codeAssets: codeAssets)
+              : FakeFlutterNativeAssetsBuilderResult.fromAssets(
+                  codeAssetsForLinking: <String, List<CodeAsset>>{'package:bar': codeAssets},
+                ),
+          linkResult: buildMode == BuildMode.debug
+              ? null
+              : FakeFlutterNativeAssetsBuilderResult.fromAssets(codeAssets: codeAssets),
         );
         final environmentDefines = <String, String>{
           kBuildMode: buildMode.cliName,
diff --git a/packages/flutter_tools/test/general.shard/isolated/native_assets_test.dart b/packages/flutter_tools/test/general.shard/isolated/native_assets_test.dart
index 9b1795cc1eb20..6926e7ece5988 100644
--- a/packages/flutter_tools/test/general.shard/isolated/native_assets_test.dart
+++ b/packages/flutter_tools/test/general.shard/isolated/native_assets_test.dart
@@ -250,6 +250,44 @@ void main() {
     },
   );
 
+  testUsingContext(
+    'Native assets: duplicate assets throws tool exit listing duplicate IDs',
+    overrides: <Type, Generator>{ProcessManager: () => FakeProcessManager.empty()},
+    () async {
+      final File packageConfig = environment.projectDir.childFile('.dart_tool/package_config.json');
+      await packageConfig.parent.create();
+      await packageConfig.create();
+
+      final File directSoFile = environment.projectDir.childFile('direct.so');
+      directSoFile.writeAsBytesSync(<int>[]);
+
+      CodeAsset makeCodeAsset(String name, Uri file, LinkMode linkMode) =>
+          CodeAsset(package: 'bar', name: name, linkMode: linkMode, file: file);
+
+      expect(
+        () => runFlutterSpecificHooks(
+          environmentDefines: <String, String>{kBuildMode: BuildMode.release.cliName},
+          targetPlatform: TargetPlatform.linux_x64,
+          projectUri: projectUri,
+          fileSystem: fileSystem,
+          buildRunner: FakeFlutterNativeAssetsBuildRunner(
+            packagesWithNativeAssetsResult: <String>['bar'],
+            buildResult: FakeFlutterNativeAssetsBuilderResult.fromAssets(
+              codeAssets: <CodeAsset>[
+                makeCodeAsset('direct', directSoFile.uri, DynamicLoadingBundled()),
+                makeCodeAsset('direct', directSoFile.uri, DynamicLoadingBundled()),
+              ],
+            ),
+          ),
+          buildCodeAssets: const BuildCodeAssetsOptions(appBuildDirectory: null),
+          buildDataAssets: true,
+          recordedUsesFile: null,
+        ),
+        throwsToolExit(message: 'Found duplicates in the code assets: [package:bar/direct]'),
+      );
+    },
+  );
+
   testUsingContext(
     'unit tests does not require compiler toolchain',
     overrides: <Type, Generator>{
diff --git a/packages/flutter_tools/test/general.shard/isolated/windows/native_assets_test.dart b/packages/flutter_tools/test/general.shard/isolated/windows/native_assets_test.dart
index 22b5ba23cb168..2a9b8e5dc2f94 100644
--- a/packages/flutter_tools/test/general.shard/isolated/windows/native_assets_test.dart
+++ b/packages/flutter_tools/test/general.shard/isolated/windows/native_assets_test.dart
@@ -86,7 +86,11 @@ void main() {
           ];
           final buildRunner = FakeFlutterNativeAssetsBuildRunner(
             packagesWithNativeAssetsResult: <String>['bar'],
-            buildResult: FakeFlutterNativeAssetsBuilderResult.fromAssets(codeAssets: codeAssets),
+            buildResult: buildMode == BuildMode.debug
+                ? FakeFlutterNativeAssetsBuilderResult.fromAssets(codeAssets: codeAssets)
+                : FakeFlutterNativeAssetsBuilderResult.fromAssets(
+                    codeAssetsForLinking: <String, List<CodeAsset>>{'package:bar': codeAssets},
+                  ),
             linkResult: buildMode == BuildMode.debug
                 ? null
                 : FakeFlutterNativeAssetsBuilderResult.fromAssets(codeAssets: codeAssets),
diff --git a/packages/flutter_tools/test/integration.shard/isolated/dart_data_asset_conflicting_assets_test.dart b/packages/flutter_tools/test/integration.shard/isolated/dart_data_asset_conflicting_assets_test.dart
index 9f485e15b2d77..d43efccfa3fd5 100644
--- a/packages/flutter_tools/test/integration.shard/isolated/dart_data_asset_conflicting_assets_test.dart
+++ b/packages/flutter_tools/test/integration.shard/isolated/dart_data_asset_conflicting_assets_test.dart
@@ -46,7 +46,7 @@ void main() {
             ..update(<String>['flutter', 'assets'], <String>[assets.keys.first])
             ..update(
               <String>['dependencies'],
-              <String, String>{'hooks': '^1.0.2', 'data_assets': '^0.19.6'},
+              <String, String>{'hooks': '^2.0.0', 'data_assets': '^0.20.0'},
             );
         });
 
diff --git a/packages/flutter_tools/test/integration.shard/isolated/dart_data_asset_flutter_build_test.dart b/packages/flutter_tools/test/integration.shard/isolated/dart_data_asset_flutter_build_test.dart
index 5664983cdc9ad..0ca503f8776c6 100644
--- a/packages/flutter_tools/test/integration.shard/isolated/dart_data_asset_flutter_build_test.dart
+++ b/packages/flutter_tools/test/integration.shard/isolated/dart_data_asset_flutter_build_test.dart
@@ -71,6 +71,45 @@ void main() {
           }
         }
       });
+
+      testWithoutContext(
+        'flutter build $target rebuilds when data asset file is deleted',
+        () async {
+          final assets = <String, String>{'id1.txt': 'content1'};
+          writeAssets(assets, appRoot);
+          writeHookLibrary(appRoot, assets, available: <String>['id1.txt']);
+          writeHelperLibrary(appRoot, 'version1', assets.keys.toList());
+
+          ProcessTestResult result = await runFlutter(
+            <String>['build', '-v', target],
+            appRoot.path,
+            <Transition>[Barrier.contains('Built build${Platform.pathSeparator}$target')],
+          );
+          if (result.exitCode != 0) {
+            throw Exception(
+              'first flutter build failed: ${result.exitCode}\n${result.stderr}\n${result.stdout}',
+            );
+          }
+
+          final File fileToDelete = dependencyRoot
+              .childDirectory('data')
+              .childFile('generated.txt');
+          expect(fileToDelete.existsSync(), true);
+          fileToDelete.deleteSync();
+
+          // Second build should re-run the build_hooks target and succeed.
+          result = await runFlutter(
+            <String>['build', '-v', target],
+            appRoot.path,
+            <Transition>[Barrier.contains('Built build${Platform.pathSeparator}$target')],
+          );
+          if (result.exitCode != 0) {
+            throw Exception(
+              'second flutter build failed: ${result.exitCode}\n${result.stderr}\n${result.stdout}',
+            );
+          }
+        },
+      );
     }
   });
 }
diff --git a/pubspec.lock b/pubspec.lock
index 01fa65203ef84..e36f442c7e5a8 100644
--- a/pubspec.lock
+++ b/pubspec.lock
@@ -150,10 +150,10 @@ packages:
     dependency: "direct main"
     description:
       name: code_assets
-      sha256: "83ccdaa064c980b5596c35dd64a8d3ecc68620174ab9b90b6343b753aa721687"
+      sha256: dad6bf6b9f4f378b0a69edbf42584d336efd1a9ce15deb1ba591cbb1b5ff440f
       url: "https://pub.dev"
     source: hosted
-    version: "1.0.0"
+    version: "1.1.0"
   code_builder:
     dependency: transitive
     description:
@@ -255,10 +255,10 @@ packages:
     dependency: "direct main"
     description:
       name: data_assets
-      sha256: d8b93648a338f471e576e0ba05f6b5d63a4e0fa447ca839a500267421d9245ba
+      sha256: "8bfdbf25ec8a0f4b5a3c993042c4ab9996ba354f0b03d40f4e360f3730d71cae"
       url: "https://pub.dev"
     source: hosted
-    version: "0.19.6"
+    version: "0.20.0"
   dds:
     dependency: transitive
     description:
@@ -502,18 +502,18 @@ packages:
     dependency: "direct main"
     description:
       name: hooks
-      sha256: "025f060e86d2d4c3c47b56e33caf7f93bf9283340f26d23424ebcfccf34f621e"
+      sha256: a41af4e8fc687cd6d33de9751eb936c8c0204ebe2bcb6c15ecf707504bf47f31
       url: "https://pub.dev"
     source: hosted
-    version: "1.0.3"
+    version: "2.0.0"
   hooks_runner:
     dependency: transitive
     description:
       name: hooks_runner
-      sha256: "248aaf6d687806959888be1bc0ab66bcf616c4f476e97cfc1b02cd97b8e06dd4"
+      sha256: b2545e50cc62b1cfcf4d94b3939a89776db72af342680d942ccad429720c4eb1
       url: "https://pub.dev"
     source: hosted
-    version: "1.2.1"
+    version: "1.3.0"
   html:
     dependency: "direct main"
     description:
@@ -718,10 +718,10 @@ packages:
     dependency: "direct main"
     description:
       name: native_toolchain_c
-      sha256: "6ba77bb18063eebe9de401f5e6437e95e1438af0a87a3a39084fbd37c90df572"
+      sha256: "49c147aa4a5905ec12028e2b7bfe360eace6cb91fe4cf08a3fe76e309592acae"
       url: "https://pub.dev"
     source: hosted
-    version: "0.17.6"
+    version: "0.19.0"
   nested:
     dependency: "direct main"
     description:
@@ -742,10 +742,10 @@ packages:
     dependency: transitive
     description:
       name: objective_c
-      sha256: "100a1c87616ab6ed41ec263b083c0ef3261ee6cd1dc3b0f35f8ddfa4f996fe52"
+      sha256: "6cb691c686fa2838c6deb34980d426145c2a5d537491cb83d463c33cdbc726ed"
       url: "https://pub.dev"
     source: hosted
-    version: "9.3.0"
+    version: "9.4.1"
   package_config:
     dependency: "direct main"
     description:
diff --git a/pubspec.yaml b/pubspec.yaml
index 97b938f8080e8..00ca815783741 100644
--- a/pubspec.yaml
+++ b/pubspec.yaml
@@ -97,7 +97,7 @@ dependencies:
   checked_yaml: 2.0.4
   cli_config: 0.2.0
   clock: ^1.1.2
-  code_assets: 1.0.0
+  code_assets: 1.1.0
   collection: ^1.19.1
   convert: 3.1.2
   coverage: 1.15.0
@@ -121,8 +121,8 @@ dependencies:
   google_mobile_ads: 8.0.0
   googleapis: 14.0.0
   googleapis_auth: 2.3.1
-  hooks: 1.0.3
-  data_assets: 0.19.6
+  hooks: 2.0.0
+  data_assets: 0.20.0
   record_use: 0.6.0
   html: 0.15.6
   http: 1.6.0
@@ -142,7 +142,7 @@ dependencies:
   meta: ^1.18.2
   metrics_center: 1.0.15
   mime: 2.0.0
-  native_toolchain_c: 0.17.6
+  native_toolchain_c: 0.19.0
   nested: 1.0.0
   node_preamble: 2.0.2
   package_config: 2.2.0
@@ -224,4 +224,4 @@ dependencies:
 dev_dependencies:
   ffigen: 20.1.1
 
-# PUBSPEC CHECKSUM: ntrh87
+# PUBSPEC CHECKSUM: 82uul6