Do you just try what @renehoj say in this post?
I try with it and all was ok for me.
and to restore the new startmenu, i just create a new launcher with qubes-app-menu for the ‘command’ in ‘properties’.
Edit: I seem to remember i had this sort of troubles with sys-gui in 4.1 and using qvm-sync-appmenus and qvm-appmenus commands in sys-gui, then, all went back to order.
Do you try this two commands in Dom0 then reboot?