It’s imperfect, but until we have a better solution for this, there’s a new --update-only flag for fly deploy as of flyctl 0.1.58 that doesn’t create machines for empty process groups. I’d like to make this better at some point, but this should unblock you for now 
(this also means, though, that if you add new process groups, that flag will prevent them from getting their machines)
Does that work for your usecase at the moment?