[[ http://i.imgur.com/ZCVpA8j.jpg | Picture of how it looks after exiting and reentering the game. ]]
when the ship disappears, you lose your ability to interact with it but you can still toggle build mode and exit it. when you exit the core the screen is still flickering, and re-entering the game doesn't help.
some more circumstances-
-the parent ship had several other subvehicles
-there was logic set up, and previously activated, to undock subvehicles. the subvehicle was manually undocked however