How to reproduce:
1. Open the attached project “IN-143010”
2. In the Project window open Assets → Scenes → “SampleScene”
3. In the Hierarchy window make sure that the “Double Click me Before enter playmode” sub-scene has the editing enabled
4. Double click on this sub-scene
5. Enter Play mode
6. Exit Play mode

Actual result: The Prefab in the sub-scene is unpacked
Expected result: The Prefab in the sub-scene stays packed

Reproducible with: 1.2.4 (6000.0.0f1, 6000.0.76f1), 1.4.7 (6000.0.76f1, 6000.3.17f1), 6.4.0 (6000.4.0a4, 6000.4.10f1), 6.5.0 (6000.5.0a1, 6000.5.0b11, 6000.6.0a6)

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

Note: The issue only reproduces on the project provided by the user