Playing as the Terran Alliance, I used my initial survey ship to attack some pirates over salvage rights to a ship graveyard. My survey ship sustained some damage in the battle, so I sent it to the nearest planet to hasten repairs. After checking on its progress a few turns latter, I could not find the ship in orbit around the planet. Though the icon showing the planet was being guarded was present, and I the ship still showed as existing in my tab showing the my list of ships game wide.

I continued to play until my technological capabilities allowed me to build surveyors of my own. However the shipyard showed a similar anomaly. Although the first model of survey ship showed up in the list of ships available to build, complete with name and mouse over tooltip, the icon representation of the ship was not present. I returned to the planet where I had set my initial survey ship in orbit for repairs and right clicked where the icon for the ship should have been: and behold, it gave me the option to eject my missing ship from orbit.