I like that you admit to borking your system! Backups are essential. Everyone has (or will) have a HDD/SSD failure or bork their drive one day. It only takes one key press!!
Similarly I have to admit to accidentally wiping the flatpak repository (var/lib/flatpak) when I was trying to change it to point to a copy in my home directory (my var partition is dumb tiny for a prior Debian bookworm install). And I was fairly early on in the setup process of my laptop environment so I hadn’t really gotten to backups being setup yet. Now I’m. Gun shy and won’t run rm -rf without adding the -i. (Solid advice I found after this booboo). And I used to WORK for a backup software company. I was able to work around the problem though. Searched my history for the 5 or 6 flatpaks I had installed so far and redid them with the new symbolic link to my home dir. worked like a charm. Now my flarpaks can be modular like my home directory.
Other systems I've used and would recommend. P5 Backup Bacula - This one is VERY involved with the server setup. AMANDA - (some people don't like this one because of the way it does/doesn't manage scheduling of backups)
Pika--- works for me ... but I like your comments on GIT ... i neeed a versioning control option since im thinking of taking my google sheets off the cloud for privacy... but at the moment dont know what i can use for versioning control apart from GIT which i learn´t about from you... thanks