Mucking around with this further - I quit Architect, relaunched it. In the opening dialogue (recent projects) there is a fullscreen toggle button. I tapped that, and then loaded my project. Lo and behold, the fullscreen button now appears in the menu and I can unfullscreen the app. I've tried to recreate the bug of the disappearing full screen button but haven't yet.
That's very odd. We've raised this issue with the Sencha Desktop Packager team and neither of our teams have been able to reproduce the issue. If you are able to find a way to reproduce it please let us know so that we can get it resolved.
Sencha Architect Development Team