Shoutout to Arq backup which simply gives you an option in backup plans for what to do with cloud only files:

- report an error

- ignore

- materialize

Regardless, if you make it back up software that doesn’t give this level of control to users, and you make a change about which files you’re going to back up, you should probably be a lot more vocal with your users about the change. Vanishingly few people read release notes.