Thank you both for you help (:
I got 15 apps using this, does this mean I have to uninstall all of them? Holy... Even preinstalled (Fedora 40 KDE) once like kiview are listed.
Also shows me these apps as using org.gtk.GTk3theme.Breeze-Dark branch 3.22when $ flatpak update
I use "software" (gnome) to install flatpaks with an UI for now. I hope they fix the bug in discover sooner or later.
I have no idea other than just to wait...
Did the trick
https://red.artemislena.eu/r/flatpak/comments/1clhrhm/flatpak_complains_about_end_of_life_runtime_cant/