Reproduction steps:
1. Download the attached "ReproProj"
2. Open ProjectA
3. Open Build Settings (File > Build Settings)
4. Go to the GeneratedScenes folder (Assets > GeneratedScenes)
5. Open each Scene in order and press “Add Open Scenes” in Build Settings
6. Repeat steps 3-5 for ProjectB
7. Close both projects
8. In downloaded ReproProj, run makelinks.sh script
9. Open ProjectA
10. Change the order of the Scenes in Build Settings
11. Close project
12 Open Shared folder (ReproProj > Shared)
13. Open EditorBuildSettings.asset
14. Observe the order of the Scenes

Expected result: Scenes order was overwritten in reflection of the changes made in step 10
Actual result: Scenes order was not overwritten

Reproducible with: 2.0.5 (2021.3.44f1), 2.4.4 (2021.3.44f1, 2022.3.48f1, 6000.0.21f1)

Testing environment: Windows 10 Enterprise 21H2, macOS 14.6.1 23G93 Darwin 23.6.0 (user reported)
Not reproducible on: No other environment tested

Notes:
- If testing with Windows, Windows Developer Mode needs to be enabled
- CQA Tested with Git Bash on Windows