How to reproduce:
1. Open the attached project “IN-138155”
2. In the Project Window, open Assets → “RegularPrefab”
3. Left-click in the Hierarchy and create a new 3D Object (ex. Cube)
4. Save the changes by pressing CTRL+S (don’t close the Prefab Mode)
5. Go to the Test Runner window (it should be opened on the right, if it isn’t: Window -> General -> Test Runner)
6. In EditMode, run the tests
7. After the test, in the Project Window, open Assets → “RegularPrefab” again
8. Observe the Hierarchy

Actual result: The 3D object created in step 3 is gone (changes are reverted)
Expected result: Running tests don’t interfere with the Prefab

Reproducible with: 2023.1.0a14, 6000.0.71f1, 6000.3.12f1, 6000.4.1f1, 6000.5.0b1, 6000.6.0a1

Reproducible on: Windows 11
Not reproducible on: Tahoe 26.3.1 (M1 max)