I have had this problem for quite some time but have never bothered to go after it.
Today, after once again losing a few scratch texts because of this ongoing issue, I have found this thread and also a few related open issues on Notepad++ Issues tracker:
Issue: Default session’s unsaved files are lost (from session’s XML file) after closing Notepad++ in a different session ‘enable session snapshot’ gets disabled occasionally Saved Sessions lost Notepad++ resets my auto-backup setting after I perform a git commit with it. Backup is broken in several ways with multiple instancesThis is particularly unfortunate because Git installer for Windows itself actually offers to set up Notepad++ as the default editor for commits.
Setting up a portable version just for this seems a bit too much, also it would then be annoying to manually keep both Notepad++ configurations in sync. It is sad, but I have decided to do the same as @Ron-Little and simply use Windows’ Notepad.exe for Git and avoid this problem altogether.