Three versions of Geary. Which should I use and can it be done?

[Photon]

@pajuky

This is why when you installed the Flatpak, you started (in the Flatpak) with a clean slate; but when you downgraded to an earlier version you still had all the files, since the older version (still a Flatpak) was looking for the Geary files in the same folder as version 44.

Try Flatsweep to clean out the flatpak detritus.