Ran fdupes -rd /home without -A, now flatpak is dead, any help?

Anyone has any ideas how to revive it? Whenever I try to run anything, I get

    
bwrap: Unable to open lock file /usr/.ref: No such file or directory
error: ldconfig failed, exit status 256

  

No logs in syslog other than an attempted launch.

Google is surprisingly unhelpful on this one. I've tried both flatpak repair and apt install --reinstall flatpak to no success. AI suggests to straight up purge flatpak entirely and start anew, but I am wary of it also taking out the app caches, logins, configs, etc, which I'd rather preserve if possible.

Distro is pop 22, btw