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The root cause of this issue are some applications which have been installed previously as part of the default system installation which are no longer supported on recent Endless OS versions.

Please open ‘Terminal’ and run (copy/paste to prevent typos):

flatpak list --app-runtime=com.endlessm.Platform/x86_64/eos3.0 --columns=app | grep "\." | while read app
do
    flatpak uninstall --assumeyes --delete-data ${app}
done
flatpak uninstall --assumeyes --delete-data com.endlessm.Platform/x86_64/eos3.0

then:

flatpak list --app-runtime=com.endlessm.Platform/x86_64/eos3.1 --columns=app | grep "\." | while read app
do
    flatpak uninstall --assumeyes --delete-data ${app}
done
flatpak uninstall --assumeyes --delete-data com.endlessm.Platform/x86_64/eos3.1

and finally:

flatpak list --app-runtime=com.endlessm.Platform/x86_64/eos3.2 --columns=app | grep "\." | while read app
do
    flatpak uninstall --assumeyes --delete-data ${app}
done
flatpak uninstall --assumeyes --delete-data com.endlessm.Platform/x86_64/eos3.2

Please let us know if that worked out.