In the practice mission I am testing I have characters go from system space to a planet surface, then into a building, back out to the planet, then back to the ship in system space.
From what I have been able to see, if your players return to a map they were previously at, you need to make a copy of that map with different encounters if you want some different to happen. For example, if the first time you are in space you have three ship encounters, and the second time you want only one encounter you have to make another copy of that map with only one encounter present.
Am I correct in this assumption? If so, there is definitely a need to be able to copy maps so that all you have to do is change the encounters.