I have yet to be able to got back to the same map without that part of the mission restarting. I would think with space being a issue finding a way to reuse the same map more then once in mission would be important. Then I might been doing something wrong.
I have run into the same issue. My only work around was to recreate the map from scatch and give it another name. Painful but it worked. Luckily I only had 6 elements I had to replace. The orginal enemy spawns were gone of course.
For as often as this functionality seems to be used in developer designed missions (or are you also redoing the maps by hand when you re-enter the system during a stage of the mission?), it's surprising this wasn't included.