If you need to grant a flatpak application access to parts of your filesystem, you can override the sandbox permissions using the following command:
sudo flatpak override <package_name_here> --filesystem=<path_here>
You should only have to do this command once; the change is persistent and the next time you open the app you’ll have access to the required directory.
You can get the package_name_here from the command flatpak list and add it in minus the <> characters. And if necessary, you can use quotation marks around the filesystem path if your path has spaces in it.