(I also wrote on matrix with the user of my smartphone, too complicate change user...) In my case with the upgrade the boot was damaged, I think that if one has flathub already in use at the time of the sync, or after having installed the flatpack package for the first time after this sync, it is prudent, before rebooting, to do a sudo systemctl restart flatpak-enable-flathub.service (only for the first reboot to avoid problems like mine).
On the other hand, in my case I still need to do sudo systemctl restart flatpak-enable-flathub.service every time after the reboot to make it work perfectly (active according to systemctl status), but at least it doesn't compromise the boot (even if "Active: failed") and I don't have the knowledge to know if this has a some real importance.
