First try a running the update with a verbose flag and see if there’s any errors flatpak update -v
If you don’t spot anything obvious, try a sudo flatpak repair and then reboot your system (or just restart flatpak-system-helper.service) and see if that fixes it.
As a last resort, you may need to uninstall all your apps using flatpak uninstall --all --delete-data
After that, you’ll have to clean clean up your ~/.var/apps, ~/.local/share/flatpak, and /var/lib/flatpak directories. You could also try running Flatsweep.