The A.I. ship designer constantly creates new designs whenever you researched significant techs and marks older designs deprecated, so you loose them. If you want to keep some early designs, just save them under a different name in the ship designer.
BTW, I may be blind but I couldn't find an option to disable the automatic ship designer at all. Is it possible?
End of puntarenas's quote
It's in the options meu somewhere. I played about the first year of the first game with it on, then got fed up with new designs popping up almost every time a tech finished. As far as I can tell, the only reason to ever use it is because it cheats (might have been fixed by now) - the auto design could put more components on a ship than you could manually.