I think there are two components to this question:
-
Backing up
We had a similar discussion that you may want to check out: Qubes Backup is Slow. In particular there we have references to what the progress in making backups incremental. -
Syncing to cloud
On this second point there isn’t really anything Qubes specific, so I would direct you towards looking at other forums for this issue. However, if you’re thinking of using syncthing, I’d recommend your read this one Syncthing in Qubes-OS