I’m experiencing a recurring issue with Flatpak applications disappearing from the application launcher (SUPER key menu) in both Fedora 40 and 41. The issue seems to follow a pattern after a failed update and language changes in Flatpak applications.
History:
Initially, I was using Fedora 40 when an update got stuck at 61%. After this, I noticed that GnuCash (Flatpak version) switched from Spanish to English, despite my system being set to es_ES.UTF-8.
I tried to reinstall the missing language pack, which led to all Flatpak applications disappearing from the application launcher.
In GNOME Software, the affected applications were no longer listed to be openable, but I could still deinstall them.
After several attempts to fix this, I reinstalled Fedora 41 from scratch.
However, the same issue reappeared after some time in Fedora 41. Again, it started with GnuCash switching to English, and shortly after that, all Flatpak apps became inaccessible from the launcher.
What surprises me most is that the programs work wonderfully at first and then suddenly disappear.
Let’s ignore the GUI stuff and get some better info from the CLI
localectl status
flatpak remotes
flatpak list --app
Have you installed the apps from Flathub or Fedoras Flatpak repo? I recommend to remove that, it might have 30% advantages but 70% disadvantages, doesnt make sense to have both.
If you remove a remote (repo) the apps will be removed along with it. If you add a new remote, nothing changes of course.
If you want to replace an app, you need to uninstall it, keep the data, and reinstall it. If you uninstall from the terminal, appdata is always kept, you need --delete-data to remove it.
Thank you for the quick answer. Here are the CLI-infos:
[marcel@fedora ~]$ localectl status
System Locale: LANG=es_ES.UTF-8
VC Keymap: de-nodeadkeys
X11 Layout: de
X11 Model: pc105
X11 Variant: nodeadkeys
[marcel@fedora ~]$ flatpak remotes
Nombre Opciones
fedora system,oci
flathub system,filtered
[marcel@fedora ~]$ flatpak list --app
Nombre ID de aplicación Versión Rama Origen Instalación
xournalpp com.github.xournalpp.xournalpp stable fedora system
Betterbird eu.betterbird.Betterbird 128.7.0esr-bb22 stable flathub system
Chromium Web Browser org.chromium.Chromium 133.0.6943.53 stable flathub system
Apostrophe org.gnome.gitlab.somas.Apostrophe stable fedora system
desktop org.telegram.desktop stable flathub system
[marcel@fedora ~]$ flatpak list --app
Nombre ID de aplicación Versión Rama Origen Instalación
xournalpp com.github.xournalpp.xournalpp stable fedora system
Betterbird eu.betterbird.Betterbird 128.7.0esr-bb22 stable flathub system
Chromium Web Browser org.chromium.Chromium 133.0.6943.53 stable flathub system
Apostrophe org.gnome.gitlab.somas.Apostrophe stable fedora system
desktop org.telegram.desktop stable flathub system
Actually I don’t know which one of the repositories I should deinstall, since betterbird, for example, is only available by flathub…
This is up to you if you like to use flathub or fedora sources. Fedora sources are made with the freedom of choice for free apps. As we not distribute closed source apps, you probably will not find packages with them preinstalled. This is also true for codecs and drivers with closed source code.
As an example you have the choice to install xournalpp as an rpm and or as a flatpak from registry.fedoraproject.org.
Open the software app and click on the app you want to check. There if it is available for several sources you can choose which you like:
big advantage of Fedora’s flatpaks: they are build from the same sources as the rpms are. Let’s say you can trust them. Flathub’s flatpaks… who knows, even a “Verified” author or publisher can potentially include malware.
If an app is available from both fedora and flathub, I would always go the Fedora one, unless it’s much older (so, yes, version from both repos may not be the same, Fedora may be lagging behind, but necessarily)
Thank you! So I deinstalled the flathub-repo and run a repair:
[marcel@fedora ~]$ flatpak remotes
Nombre Opciones
fedora system,oci
[marcel@fedora ~]$ flatpak repair
Working on the system installation at /var/lib/flatpak
[12/12] Verificando fedora:runtime/org.fedoraproject.Platform/x86_64/f40…
Comprobando remotos...
[marcel@fedora ~]$ flatpak list
Nombre ID de aplicación Versión Rama Instalación
xournalpp com.github.xournalpp.xournalpp stable system
fedoraproject plataforma org.fedoraproject.Platform f40 system
fedoraproject plataforma org.fedoraproject.Platform f41 system
default org.fedoraproject.Platform.GL.default f41 system
fedoraproject plataforma traducciones org.fedoraproject.Platform.Locale f41 system
Apostrophe org.gnome.gitlab.somas.Apostrophe stable system
[marcel@fedora ~]$ flatpak run com.github.xournalpp.xournalpp
bwrap: Can't mkdir parents for /usr/lib64/GL: Read-only file system
As you can see, I still cannot start any program due to read-only restrictions.
