I upgraded to F43 using DNF System Plugin. After which some of my previously installed flatpaks will not run with the error:
bwrap: Can't mkdir parents for /home/${user}/.var/app/${app-name}/config/user-dirs.dirs: No such file or directory
(where ${app-name} is replaced with the literal application name). I didn’t track what version of flatpak existed prior to the upgrade, but am now runnning 1.16.1.
They are ‘system’ installed (vs user) and I’ve attempted to reinstall them both at system and user scope.
Did they exist also after upgrading to F43, before starting the app? Can you check for other Flatpaks installed system-wide, which you might not have started since the upgrade (i.e. not by running the Flatpak, but rather by checking the /home/${user}/.var/app/${app-name} folders.
If the folders are there, maybe something different with the permission sets? Or something specific to your setup (user migrated, systemd-homed etc)?
I have 12 system flatpaks, only 2 of them do not start. My plan of action is to start looking at runtimes/dependencies and dig into the packaging itself.