Hi,
Does anyone have the same issue? On terminal there is no updates.
On GUI even when I update they show again. I’ve used flatpak repair, reinstall packages.
And still nothing. Any tips?
BTW solution from this thread do not work for me:
https://forum.manjaro.org/t/package-manager-shows-flatpak-updates-that-dont-disappear/168784
flatpak update gives me “no updates are available”.
Have you tried
flatpak update
?
For some reason there was a report of flatpak update --system being ‘the fix’, but by default flatpak update should update both user and system REFs.
You can disabling this info’s when you open Pamac>Preferences>Third Party>Flatpak and disable Check for updates.
I’ve had this issue with every new installation I’ve done in the past four or five months—and there have been many as I’ve tested, learned, and changed my mind about things then reinstalled across my three PCs. Fortunately, the issue is more annoying than anything else.
Although I have no proof, I believe the problem happens when installing many applications at once, mixing those from the official repositories with flatpaks.
I do not have a definitive fix. I have taken a shotgun approach rather than a measured and documented one. Eventually, the problem has gone away.
Two things I have done that maybe worked and maybe did not but are not mentioned here or in the other thread are:
Clean YAY, Pacman & Pamac cache: sudo yay -Scc
Clean flatpak cache: rm -rfv /var/tmp/flatpak-cache-*
(The above taken from @Teo ’s very handy Manjaro Cheatsheet as a Menu.
[My Manjaro cheatsheet in a menu form]
Note: Read his source to find and install the dependencies, as well as any of the applications executed by the menu choices. Not all are in the base distribution.)
HTH!
It didn’t work 
flatpak update --system, flatpak update, as normal, using sudo. Updates are still there.
I know I can turn them off but I want to have notifications about update so it’s the last resort.
Nothing works bump