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Fixed in 2021.1.X
Fixed in 2019.4.X, 2020.2.X
[Prefabs] Applying added GameObject to prefab from context menu makes its scripts lose references
How to reproduce:
1. Open the attached project "1237942.zip"
2. Open the "test" scene
3. In Hierarchy window right-click GameObject "Sphere" and then click "Added GameObject" > "Apply to Prefab"
4. Undo last step (ctrl/cmd + z)
5. In Hierarchy select GameObject "Prefab GO" and in Inspector window click "Overrides" > "Apply All"
Expected result: in step 3 and 5 - GameObject "Sphere" component Test (Script) keeps the reference to the "Cube" GameObject
Actual result: in step 3 - GameObject "Sphere" component Test (Script) loses the reference to the "Cube" GameObject
Reproducible with: 2018.4.21f1 2019.3.10f1, 2020.1.0b5, 2020.2.0a7
Not reproducible with: 2017.4.39f1 - GameObject context menu does not contain "Added GameObject"
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Resolution Note (fix version 2021.1):
The issue has been fixed and should no longer reproduce in Unity 2021.1.0a7 and above.
Resolution Note (fix version 2019.4):
The issue has been fixed and should no longer reproduce in Unity 2019.4.18f1 and above