Reproduction steps:
1. Install p4merge
2. Set the p4merge as a fallback tool for unknown files in the Unity Editor’s “/Contents/Tools/mergespecfile.txt“ file
3. Extract the attached “IN-106956_TestFiles.zip“ archive
4. Open it inside the terminal
5. Locate and copy the path of the UnityYAMLMerge executable inside your Unity Engine folder
6. Execute the “{path to UnityYAMLMerge executable} merge -p "Base/YamlTest.cs" Left/YamlTest.cs Right/YamlTest.cs Merged/YamlTest.cs“ (the command might need some minor modifications depending on the platform)
7. Exit the p4merge tool without saving the merged file
8. Open the properties of the “Merged/YamlTest.cs“ file
9. Observe

Expected result: The file is left unmodified with the merge conflicts
Actual result: The modified time of the file has changed and the file is now 0 bytes long

Reproducible with: 6000.0.54f1, 6000.1.14f1, 6000.2.0b12, 6000.3.0a3

Reproducible on: M1 Max MacOS 15.5 (Tested by CQA), Windows 11 (User’s platform)
Not reproducible on: No other environment tested