Cannot update flatpak packages - Lemmy.world

Hi, I am having this strange issue where the flatpak would say that it is updated successfully, but the packages remain in the list of available updates. The packages still works. And I have tried flatpak repair --user, to no success. This propably due to the fact that I have to restore my home folder from a backup, via Déjà Dup. And I assuming there is a conficting cache file some where?