I use scp just to copy the config and storage directories. That's really all you need to from Reactor to get it going on a reinstall, as you've seen.
I find file-based backups of entire Linux systems to be perilous, because permissions, links and special files almost always get screwed up somehow, so I never recommend that route. An image backup is better (I use partclone to back up used space only, and it's good about the later target system being a different size/geometry than the original/source), but I'll only do that maybe 1-2 times per year. I figure if I can restore an image quickly and apt-get update my way back to current, that's fast enough on recovery.