Failing to remove old gnome-authenticator
I did an 'apt-get remove gnome-authenticator' and then installed the flatpak version.
Now I have two identical "lock" icons on the desktop.  One brings up the flatpak version 4.x and the other brings up the 3.x version.
I can find no remnants of gnome-authenticator via apt-get or 'dpkg -l' and yet the icon and the program remain.
Any idea how to get rid of the 3.x version?
You could check the corresponding .desktop file in /usr/share/applications/, see which executable it points do and then look up the package ("dpkg -S $filename"). Or you could manually remove the old .desktop file to get rid of the icon.
Looking in /usr/share/applications for a .desktop file did not succeed. In fact I could not find a reference to either gnome-authenticator in there.
While dealing with a different issue I came across the 'list of application' in settings, which showed the duplicate authenticators also and suggested 'open in software'. So I did that and found myself at another list of applications. I selected 'Installed' and the two gnome authenticators showed there with little [x] buttons. They were basically indistinguishable other than by the size of the application, so I picked the smaller one size wise and tapped the [x]. It asked me to confirm and now the extra gnome-authenticator is gone from the desktop.
I also guessed right and the flatpak one is the one that remains.

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