As an equal-opportunity employer, my notes on completely removing flatpak (may God have mercy on my soul):
Before starting, be sure to inventory what's installed:
$ flatpak list
Then run the following commands to remove all flatpaks and the flatpak service:
$ flatpak uninstall --all
$ sudo apt purge --autoremove flatpak
After performing these operations, go over and rm -rf /var/lib/flatpak.
At least a logout and login will probably be needed to help the system forget it ever had flatpaks, especially if you're running a desktop manager like Gnome Shell.