Reproduction steps:
1. Open the attached “BugRepro” project
2. Open the “Assets/Baking/BakingDependencies/BakingDependencies” Scene
3. In the Hierarchy window, enable the “BakingDependenciesSubscene” Subscene’s Auto Load Scene checkbox
4. Select the “Smiley” GameObject
5. Enter Play Mode
6. In the Scene view, move the GameObject using the Move Tool
7. Exit Play Mode
8. Observe the “Smiley” GameObject’s position

Expected result: The GameObject has reset to the position before step 6
Actual result: The GameObject remains in the same position

Reproducible with: 1.0.16 (2022.3.50f1), 1.3.2 (2022.3.50f1, 6000.0.23f1)

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