I wonder if this may reveal anything?
journalctl -xe | grep flatpak
You are not running low on disk space by any chance?
I don't use Flatpak or Snap myself, so others may be better source of help.
EDIT: This thread is similar. May be worth a read, but no specific "Solution" was marked. Flatpak just disappeared with all of the installed apps - #8 by Ponce-De-Leon