Sorry I originally posted around permissions as I misunderstood; deleted that. The solution is below:
If it's a user installed flatpak you should find the config files in:
~/.local/share/flatpak/overrides
Edit the document for the flatseal app. Thats where flatseal or the flatpak override tool makes it's config changes for user installed flatpaks (including env overrides). You can also delete the flatseal file (which will be the name of the flatpak - com.github.tchx84.Flatseal) "to set back to default.
There will only be a few files - files are only created when there are overrides set. Anything running default permissions/config won't have an override file.
EDIT: For completeness, for System wide flatpaks all the files are in:
/var/lib/flatpak
Just to explain why they're stored there: you're trying to change the config of the sandbox itself not the app. Flatpak manages the sandbox and it is flatpak that needs to know what permission an app should have. Any files in "~/.var/app/..." pertain to the app itself inside it's sandbox.