That seems like a pretty straightforward issue to solve, to simply backup only those files that are actually on the system, not the stubs. If it's on your computer, it should able to get backed up. If it's just a shadow, a pointer, it doesn't.

Making the change without making it clear though, that's just awful. A clear recipe for catastrophic loss & drip drip drip of news in the vein of "How Backblaze Lost my Stuff"