alt Hacker NewsThis is a pain, to be sure, but surely there is some sort of logic you could implement to detect whether a file is a Real File that actually exists on the device (if so, back it up) or a pointer to the cloud (ignore it by default, probably, but maybe provide a user setting to force it to back up even these)
It used to be the case that placeholder files were very obvious but now OneDrive and iCloud (possibly others) work more like an attached network storage with some local cache, and that was a good move for most programs because back then a file being evicted from storage looked like a file deletion.