Yeah, I remember trying to delete a fully loaded Python installation that had found its way onto a OneDrive-managed folder. After a chat with IT, I learned that OneDrive can only delete X number of files at once. We agreed that the most practical solution was for me to spend an hour deleting files by hand, and choose another drive next time. Fortunately I don't really depend on OneDrive as a backup, since GitHub does that job well enough.

The other thing is that both Git and OneDrive are in some sense fiddling with your file system at once.