That command flatpak uninstall --unused should not remove anything necessary. The latest version of the nvidia pak should be the only one needed since that is likely the drivers you have installed.
I just removed 4 versions with my update and installed the newest.
Unlike dnf or rpm-ostree a flatpak update only upgrades the already installed paks and installs newer ones (though it did remove 2 of 31 for me). The uninstall seems needed to remove all the unused ones.