Invalid GameObjects are created in the Hierarchy when removing a nested GameObject's parent by replacing a Prefab variant

Steps to reproduce:

1. Open the attached “IN-140165” project
2. Open the SampleScene
3. Select the “Canvas 1” GameObject in the Hierarchy
4. In the Inspector, change the “Prefab” field to the “Test” Prefab variant
5. Select the “Canvas 2” GameObject in the Hierarchy
6. Select the “Test” GameObject in the Hierarchy
7. In the Inspector, change the “Prefab” field to the “Canvas 1” Prefab
8. Observe the Hierarchy

Actual result: Another “Canvas 2” GameObject is added. One of them will show a blank Inspector and cannot be deleted
Expected result: Only one “Canvas 2” GameObject is present

Reproducible with: 6000.3.0a2, 6000.3.17f1, 6000.4.0a3, 6000.4.11f1
Not reproducible with: 6000.0.77f1, 6000.3.0a1, 6000.5.0a1, 6000.5.0b12, 6000.6.0a7 (“Canvas 2” disappears after step 4)
Fixed in: 6000.5.0a1

Reproducible on: Windows 11
Not reproducible on: No other environments tested

Notes:

• Only reproducible when using the New Hierarchy Window (Edit → Preferences → General → Use new Hierarchy Window)
• The “Canvas 1” Prefab contains the nested “Canvas 2”, while the “Test” Prefab variant does not contain the “Canvas 2” GameObject
• Reloading the scene removes the invalid GameObject
• The extra GameObject is not created unless the “Canvas 2” GameObject is selected in step 5. However, the GameObject is already invalid in this step
• The reporter experienced a crash using similar reproduction steps. However, CQA was unable to reproduce the crash
• Right-clicking the invalid GameObject produces a NullReferenceException