

Use a git repo and stow
tool. For updating, you only need run git pull
(and stow
if you create config for a new software). If you modify some config, just git add && git commit && git push.
With this way, you can also record change history of your config.
It looks like because the sandbox of Flatpak prevent the program access the unix domain socket of pcscd.
There is a document on Arch Wiki.
https://wiki.archlinux.org/title/Desktop_entries