I finally found a workaround.
Run flatpak permissions desktop-used-apps | grep Vivaldi and check that the wrong app is in the "Permissions" column. It should be something like this:
Table Object App Permissions Data
desktop-used-apps application/pgp-keys com.vivaldi.Vivaldi org.kde.kwrite,1,3 0x00
desktop-used-apps x-scheme-handler/zoommtg com.vivaldi.Vivaldi org.kde.ark,1,3 0x00
In this case, I am interested in the second row. The "Object" contains the mime-type of interest.
Run flatpak permission-remove desktop-used-apps x-scheme-handler/zoommtg, replacing x-scheme-handler/zoommtg with your custom mime type.
Done!
P.S. It's a shame that Vivaldi doesn't provide a menu ala Firefox for resetting such file associations, though...