Just an example:
- You install a fedora-41 template. The default terminal is
gnome-terminal - You create an application qube, based on that template. The shortcut called Terminal works because it points to
gnome-terminal - After that, you install fedora-42-xfce, the default terminal is now
xfce4-terminal - You change the template of your app qube. Now, the Terminal shortcut doesn’t work. It still points to
gnome-terminalbut fedora-42-xfce usesxfce4-terminal. - If you remove the missing Terminal from the applications and add again the new one (pointing to
xfce4-terminal) it should work.
Qubes OS has no way to handle it automatically; you have to do it by hand with your old application qubes.
Try to create a new application qube and see if your shortcuts work.