Saved me for the second time in 6 months, holy shit.
Flatpak problems seem to keep happening on my machine, and this time I just couldn't do anything with flatpak at all. Apps wouldn't launch, terminal commands wouldn't work. No browser, communications, email, nothing since everything is now on flathub.
Thankfully I had backups set up. One is timeshift, which incrementally saves my system and boot files, and the other is the distro's own Backup tool, which is a bit slow but saves my entire home directory every few days.
I was able to restore the missing files from the backup, and everything works again. I'm now going through the issue to figure out how exactly it happened.
Last time flatpak decided to just delete its own PGP keys so it couldn't communicate with itself anymore. A timeshift backup fixed that - I have since set up hourly backups over 24 hours, since they're incremental they don't take up a lot of space and they delete the older ones automatically. Default home backup app takes a bit more space, I'm going to look at replacing it with something a bit leaner and faster if possible.
Still took a bit of time, but we're talking maybe 15 minutes instead of a potential multi-day or even week-long headache.
But if you're switching to linux, do yourself a favor and get a spare 1TB drive that you will use exclusively for backups. It's not optional, this will literally save you.
If you want to do cool shit you can even set up a NAS in your basement and backup on there, otherwise honestly even just an external drive you plug in is enough, as long as you remember to do at least daily backups.
Btrfs snapshots have saved me from bad updates and dumb config changes.
But backups are essential for responsible computer usage.