I have steam version. I tried to reinstal game several times but it dasn't help.
P.s I don't know where exactly are saved games so I can't do anything.
Go to your Steam folder which is probably:
X:\Program Files\Steam
and look for this folder structure:
Steam\steamapps\common\galactic civilizations ii - ultimate edition
Perhaps the saved games folder is there and the 'ships' folder therein somewhere.
I have the Space Unlimited version and the saved games folder for GC II was under 'Documents and Settings' somewhere (XP SP3). Can't remember exactly where as just re-installed my 2 operating systems very recently and haven't installed the game back again, but IIRC the GC II folder was actually called something like GC2UL. I think the 'ships' folder was in there but not sure. I remember seeing a load of .xml files from designs made in game.
Either way, just do a search for ships on your computer? LOL