How to Reproduce:
1. Create a new cloud project using the Universal 3D template in Unity Hub
2. Open Unity version control window
3. Create Workspace with "I need branching, merging, and the ability to push/pull (Unity UVC workspace)" option selected
4. Create a MonoBehaviour script (eg. TestFile.cs)
5. In Unity Editor, under "Unity Version Control" Window, inside "Pending Changes", click "Check in"
6. In TestFile.cs scriptwrite Debug.Log("A1"); in the "Start" fnction and save the script
7. In Unity Editor, under "Unity Version Control" Window, inside "Pending Changes", click "Check in"
8. Under "Unity Version Control" Window, in "Changesets" tab, right click on the Second latest changeset and choose "Switch workspace to this changeset"
9. Open "TestFile.cs" script and write Debug.Log("A2"); in "Start" function and save the script
10. In "Unity Version Control" Window, inside "Pending changes", click "Check in"
11. Right click on the resulting conflict of TestFile.cs and click "Merge keeping the incoming changes (head/source)"
12. Go back to "Pending Changes" tab and observe changed items
Actual Result: "TestFile.cs" is present in "Changed items"
Expected Result: "TestFile.cs" is not present in "Changed items"
Reproducible with: 2.5.1 (6000.0.0f1), 2.12.4 (6000.0.0f1, 6000.6.0a7)
Couldn't test with: 2.3.1, 2.4.3, 2.4.4 (Could not create workspace)
Reproducible on: Windows 11
Not reproducible on: No other environments tested