Oof. Ok, so I looked into Space Exploration a bit, and it looks like it just deletes everything and recreates it when the ship lands. So it's an entirely different character entity. I will talk to the developer and see if they can fire off an event when this happens to make this a smooth transistion.
As for what to do in the meantime, don't spawn avatars on ships or use the control center on ships.
If you end up in a stuck state and no way to swap back to your body (and no saves that work), you can run this command to spawn a new basic character and swap to it. You will likely have an old one standing around, but killing it should drop it's equipment.
/c remote.call("Avatars", "create_new_body")