Reproduction steps:
1. Open attached project "SmartMerge_TestSetup.zip" in version that's to be tested
2. Setup UnityYAMLMerge (https://docs.unity3d.com/Manual/SmartMerge.html)
3. Create new GitHub repository, check it out, add the project to Trunk and Commit the changes.
4. Open the project located within the checked out repository and scene "SampleScene"
5. In Hierarchy window, duplicate "SouthArea" GameObject, select it
6. In Inspector window, rename the GameObject to "WestArea"
7. Save the changes
8. In File Explorer, commit the SampleScene.unity modification via TortoiseSVN
9. In File Explorer, right-click SampleScene.unity and choose TortoiseSVN -> Show Log
10. In TortoiseSVN window, right-click the first commit and select "Update item to revision"
11. In Unity Editor, observe that SampleScene.unity no longer has the "WestArea" GameObject
12. In Hierarchy window, duplicate "SouthArea" GameObject, select it
13. In Inspector window, rename the GameObject to "EastArea"
14. Save the changes
15. In File Explorer, right-click the scene file and click "SVN Update"
16. Observe TortoiseSVN window

Expected result: No conflicts
Actual result: Changes conflict

Reproducible with: 2018.4.35f1, 2019.4.28f1, 2020.3.11f1, 2021.1.10f1, 2021.2.0a19