Reproduction steps:
1. Open attached project "1299744.zip"
2. Open "SampleScene"
3. Create a new GameObject in the Hierarchy window
4. Drag new GameObject to Assets folder in Project window to make it into a Prefab
5. Save the Scene
6. Delete newly created Prefab from Assets folder
7. Reopen "SampleScene"
8. Drag GameObject to "Parent"
9. Save the Scene and reopen it

Expected result: No Recovery GameObject is created after reopening a Scene with missing Prefab as a child of other GameObject
Actual result: Recovery GameObject is created after reopening a Scene with missing Prefab as a child of other GameObject

Reproducible with: 2020.1.12f1, 2020.1.17f1, 2020.2.0f1, 2021.1.0a10
Not reproducible with: 2018.4.30f1, 2019.4.17f1, 2020.1.11f1