All of my installed apps from flathub along with the flatpak just vanished into thin air. No warnning, nothing. I just opend up my laptop saw half of my applications including the built in GUI software application just gone.
After, researching for a bit I have found out that its may have somthing to do with "GNOME 46 runtime" no longer being supported by flatpak. In fact it's expired in April 2025 I think.
Now, I am just screwed and really disappointed about the whole situation. I always update my system, so that I don't have to face issues like this. But who knew that the system itself is too old to be useable.
Now, I really don't know what to do other than reinstalling 60% of my
installed softwares.
This only deals with regularly scheduled updates. It would not, under any circumstances, suddenly remove all of flatpak and the installed packages from your computer.
In terminal, run the follow commands and please relay the output here:
Thanks man, I really appreciate your willingness to help. But you see, even my system settings (gui) are gone and I am in an urgency today. So right now I am about to do a fresh install on my laptop. Again thank you.
Remember, apps from Snap and Flatpak, being self contained, tend to be rather large. Always keep an eye on disk space if you use many Flatpaks and have limited disk size.
If you can launch Disk Analyzer from the applications menu, you can see how much of the drive is being used and how exactly is being used.
The /var directory is most likely the culprit, but I still find it strange that this would start deleting things at random. My first thought was actually some sort of failure with the drive itself.
That is a Dependency for Flatpaks. These will be updated by the Flatpak Developers because this is in their Resposibility. But even when this isn't updated, it should not delete all of the Flatpaks.