I am using bluefin-dx:stable. I search geary for example in the software center, it does not show up. But in command line flatpak search geary it does show up.
I use pkill gome-software to quit and ps aux | grep gnome-software to make sure of it. I then try flatpak update --appstream and then log out. But the problem is still there.
I’m not sure why, but as described in my question, I’ve noticed that this situation only occurs when connected remotely. When using Bluefin in person, in front of the machine, it displays normally.
I noticed the same, Flatpaks do not show in Software Centre when using remote desktop, when using from the proxmox console they show ok. Flatpaks install from the command line and warehouse remotely.