After updating the debian-12-xfce template, all flatpak packages cannot be opened, and attempts to update flatpak and uninstall and reinstall are ineffective. Error: bwrap: Can’t mount proc on /newroot/proc: Operation not permitted
error: ldconfig failed, exit status 256
zsh: exit 1 flatpak run org.telegram.desktop.
not sure it helps you, but this looks like a bug in the binary realpath 
Did you install the flatpak as user or in the template?
Is the binary realpath available on your system? (it should)
I installed flatpak in the template to normal permissions. Do I have to install it in appvm as well?
No, it was just a wild guess.
Can you try flatpak repair?
Tried it and still can’t open all the software.
could you try to run a flatpak program from a bash shell? Just to be sure it’s not zsh doing something weird in the process.
With bash it works fine, with zsh it doesn’t. I can’t open the software by double clicking on the icon, but I can open the software via the bash command line, do you have any idea how to make zsh work?
are you using a clean zsh profile or did you make a lot of change? Would it work with an “fresh” zsh environment?
I reinstalled zsh but still can’t open the flatpak software.
This must be a bug either in zsh or flatpak side, you should report this upstream now as we figured the potential root cause.
And by a clean zsh profile, I meant with no custom zshrc or zprofile file (in case you had any).