If your node isn't running, can't you simply drag & drop the updated blockchain to the other node's database directory? Won't this simply replace the missing files?
Honestly, I've never tried this for fear corrupting the data, so I copy the entire current blockchain to an external HD or SSD (whichever I have available), but first I delete the outdated backup because it's less than 2tb available.
For Linux, that's what rsync is for. But note that different Bitcoin Core downloads don't have the exact same blocks files, so if you're trying to "complement" one node with data from another note, it could still require copying almost everything.
So there's nothing I can do to optimize how backups are handled, right? I've already considered that possibility.