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Fixed in 2021.1.X
Fixed in 2019.4.X, 2020.1.X, 2020.2.X
Reference to the root prefab child is lost when pressing "Unpack Prefab" on root prefab and entering Play mode
How to reproduce:
1. Open attached project "New Unity Project.zip" and scene "SampleScene"
2. In Hierarchy window, expand "Root" object and select its child "Nested"
3. In Inspector window, GameObjectReference(Script) -> press on "Part of Root" (this highlights the "Part of Root" in the Hierarchy window)
4. In Hierarchy window, do "Unpack Prefab" for "Root" prefab
5. Enter Play mode
6. Repeat steps 2 and 3
Expected result: the "Part of Root" object in the Hierarchy is selected
Actual result: nothing is being highlighted, double-clicking on the "Part of Root" in the Inspector, opens up "Root" prefab
WorkAround: Apply the reference to prefab after the outer prefab was unpacked (this will not change the asset because the link now points to scene object and preserve the link to scene object).
Reproducible with: 2018.4.28f1, 2019.4.13f1, 2020.1.10f1, 2020.2.0b8, 2021.1.0a1
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Resolution Note (fix version 2021.1):
Fixed in 2021.1.0a4
Resolution Note (fix version 2020.2):
Fixed in 2020.2.0b12
Resolution Note (fix version 2020.1):
Fixed in 2020.1.14f1
Resolution Note (fix version 2019.4):
Fixed in 2019.4.16f1