Steps to reproduce:
1. Open attached project "ScriptableObjectToAssetBundleTest.zip"
2. In file menu bar click "Test->BuildAssetBundle" and go to <projects location>/AssetBundle and see "test_assetbundle" created. Note its creation time
3. In file menu bar click "Test->TouchPrefab". Prefab's "PrefabSample" X value will be increased by one
4. Exit Unity (without saving!) and open the same project again
5. Note that "PrefabSample" X value is the same as you left it
6. In file menu bar click "Test->BuildAssetBundle". Go back to <projects location>/AssetBundle and take note that "test_assetbundle" has not been updated. Creation time is the same as it was originally

Expected result: After modifying asset bundles prefab and rebuilding it, it is rebuilt
Actual result: Prefab was ignored

Note: Asset bundles does get rebuilt if you save a scene or project before quitting Unity
Building asset bundle for Unity 5.4 require modified 91 line in the script "ScriptableObjectToAssetBundleTest". Replace it to: "BuildPipeline.BuildAssetBundles(assetbundle, BuildAssetBundleOptions.None, BuildTarget.StandaloneWindows64);"

Tested and reproduced on:
Windows 10
Unity 5.1.4f1, 5.2.4p1, 5.3.3p3, 5.4.0b9