There is no code in either the installer or the game itself that could possibly delete your ships.
Check Documents\My Games\Cosmoteer\Saved Ships to see if there is anything in there.
How long has it been since you last played? What version were your playing?
Occasionally people have claimed that the game deleted their ships, but it has so far always turned out to be some other problem, like they were playing on a different user account or their computer got wiped.