How to reproduce:
1. Open the user's attached project
2. Open 'SampleScene'
3. In the Hierarchy expand the 'Parent' object
4. Right-click on 'Test Game Object' and select 'Duplicate'
5. Delete the original copy of the 'Test Game Object'
6. Save the Scene
7. Reopen the Scene
8. In the Hierarchy expand the 'Parent' object

Expected result: The '--- Last Game Object ---' is the third child of the 'Parent' object
Actual result: The '--- Last Game Object ---' is the first child of the 'Parent' object

Reproducible with: 2018.4.32f1, 2019.4.20f1, 2020.2.4f1, 2021.1.0b7, 2021.2.0a4

Notes:
- The issue is not reproducible when there are no Prefabs in the Scene