I originally posted this on reddit, but am posting here as well:
Adding flathub
Enable the flathub remote
flatpak remote-modify --no-filter --enable flathub
If it doesn’t exist, run
flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
Changing remotes of applications
Run this command to reinstall fedora flatpak repo applications with ones from flathub
flatpak install --reinstall flathub $(flatpak list --app-runtime=org.fedoraproject.Platform --columns=application | tail -n +1 )
Remove the fedora flatpak repo.
flatpak remote-delete fedora
Make sure that the only thing prompted for removal is the runtime, if any other application is listed, run
flatpak install --reinstall flathub name.of.application
Otherwise, just hit y