My commander disappeared after I changed the planet destination in mid orbit to a different planet. He arrived at the correct planet but then disappeared when he was supposed to be in that planets orbit. Know he was still alive as all of my other units got destroyed but still had the commanders metal/energy coming in. Could not locate him anywhere in the solar system. Couldn't win/lose the game, ended up having to just quit it.
Happens to me too, except usually he just disappears in orbit. Usual result still occurs, except when my base blows up I lose. No idea what the game treats him as as I usually use it as a way to get a headstart on my opponent with free resources and to fortify the new planet like hell.
