Debian-provided applications store their config and resource files in a different folder than Flatpak applications.
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.
Another thing to keep in mind, Geary v44 and Geary v43 are also closely tracking GNOME version (the desktop environment and all base libraries). So if Geary was your only v44 GNOME application, it might be worth to run
flatpak uninstall --unused
to get rid of the GNOME v44 runtime that might be taking a lot of space on your storage without getting any use at all…