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A little-known (and destructive!) feature of Flatpak: you can remove the data leftover from all apps that have been uninstalled with the command "flatpak uninstall --delete-data". By default, your user data is left untouched when you uninstall an app.
Specifically this removes data stored by the app in ~/.var/app/$APP_ID (the default writable location for per-app data) and also resets any overridden permissions.
You can also remove your user data (and reclaim some disk space) during an app uninstall by including "--delete-data" on your "flatpak uninstall $APP" command line.
The "--unused" option of the "flatpak uninstall" command is also worth checking out if you want to reclaim disk space, at the cost of potentially having to re-download runtimes later if they become needed again.