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Prefab Instance's Serialized Fields are not saved when changing them via Custom Editor Window
How to reproduce:
1. Open "Scene" scene in the attached "TestObjectsNotSaved.zip" project
2. Open Window > CUSTOM
3. Press "Assign random ID" in the opened Window
4. Observe the value on the "RndIdNoChild" GameObject's "SaveValue" Component, it should not be 0
5. Save and Reload the Scene
6. Observe the value on the "RndIdNoChild" GameObject's "SaveValue" Component
Expected Behavior: The value is saved after pressing the "Assign random ID" button and reloading the scene
Actual Behavior: The value is not saved(reset to the previous)
Reproducible with: 2017.4.20f1, 2018.3.5f1, 2019.1.0b3, 2019.2.0a4
Note: Inspect the "RndIdNoChild (1)" GameObject. It's value is saved every time, as it is not an instance of the Prefab.
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