If you're literally just replacing the command station by building a new one without scrapping or losing the first one, I don't think it's supposed to do the auto-kill-mobile-builders-and-colony-ships-thing.
If you lose the station or scrap it, then yea, the mobile builders (and colony ships) go bye-bye.
Edit: in the "replacement" case above, the first command station is quietly removed, you don't wind up with two on one planet.