My experience of changing settlements was simpler than dersvr - I just flew to another planet (via a black hole), got a map from the map alien in the space station (5 nav data) and activated it in space, flew to the planet, then settlement and become overseer.
No need to shuffle missions or anything around. It might be because I flew far enough away from the original to reset things. Does it come up with an error if you try to make a new settlement other than the warning about losing the previous one?
Shame about the 1 settlement at a time limit (thanks dersvr for confirming).