Reproduction steps:
1. Open the attached "New Test Project" on both machines
Steps on machine 1:
2. Create a new workspace in the Unity Version Control window
3. Commit the Project to the workspace
4. Disable "Auto Refresh" (Edit > Preferences > Asset Pipeline)
5. Open the "Script" Script and uncomment line 7
6. Open the "Scenes/SampleScene" Scene
7. Select the "GameObject" GO in the Hierarchy window
8. Set the "Test Bool" variable to "True" in the Inspector window
9. Save the "SampleScene" Scene
10. Commit the made changes in the Unity Version Control window
Steps on machine 2:
11. Repeat step 3
12. Open the "Scenes/SampleScene" Scene
13. Update the Project from the Plastic SCM
14. Right-click on the "Script" Script in the Project window and press "Refresh"
15. Select the "GameObject" GO in the Hierarchy window
16. Observe the "Test Bool" value in the Inspector window

Expected result: The "Test Bool" variable is set to "True"
Actual result: The "Test Bool" variable is set to "False"

Reproducible with: 2020.3.47f1, 2021.3.22f1, 2022.2.14f1, 2023.1.0b11, 2023.2.0a9

Reproducible on: Windows 10

Note:
- After reloading the Scene, the "Test Bool" variable is set to "True"