Thanks for bringing this up, pantera1989!

Pressing the Deactivate button in the (De-)Activate tab will delete the hildon.menu file - which will then automatically be replaced by the default hildon.menu file. It's a nifty failback system native to hildon already.

So to play it save, just don't close the application until you affirmed that your application menu is still working and everything should be fine.
(When I manually messed up my hildon.menu, all running applications where still fully functional - I could just not start any new.)

Thanks again, I'll add that to the first post.