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Status: Fixed in Unity 5.4.3
AssetDatabase.SaveAssets() not saving changes made to a prefab
AssetDatabase.SaveAssets() not saving changes made to a prefab inside OnPostprocessAllAssets(), but saving the scene manually applies those changes to the prefab.
1. Open the attached project
2. Open the "TEST" scene
3. Import the attached file "Prefab.prefab" into the project
4. After the "Prefab.prefab" is imported open it with any text editor outside the project
5. Notice that m_PlayAutomatically' is set to 1 even though it should be changed to 0 by Editor script "NormalizeAssets"
6. Save the scene manually
7. Open "Prefab.prefab" with any text editor outside the project again
8. Notice that m_PlayAutomatically' is set to 0 now
Reproduced on: 5.5.0b4, 5.4.1p1
Not reproducible on: 5.3.6p5
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