Steam game updates or flatpack updates (updates from the desktop store outside of Steam)?
All the Linux updates, not the game updates. I don't know if they're all flatpak, but I have tons of them waiting to update
I don't know if they're all flatpak
They should be, the Steam Deck updates system components separately through steam.
As a diagnostic step, you might wanna run flatpak update in a new Konsole window to see if there are any errors that Discover might not be telling you about.
SteamOS updates can also be done by Discover now. But I would assume his problem is the flatpak updates.
To fix flatpak issues, there is a flatpak repair command.
You mean Flatpak updates installed from Discover, right? I had issues with that as well, usually related to Deck entering sleep mode while the updates are running. The cause is that the systemd service isn't running properly and needs to manually shut downj and launched (not a system reboot). I try to remember to look up what the exact command was when I'm back home. Reply to this comment if I forget to.
Run systemctl restart flatpak-system-helper.service after the already mentioned flatpak repair command.
Are you able to share a screenshot of the update that’s failing?
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