Ship designs/custom civilizations won't stay deleted

When I make custom ships the designs will only delete for the current runtime. If I exit the game and restart it they always come back, some of them come back with duplicates. I have about 50 custom ship designs and its becoming annoying to scroll through all of them to find what I want or delete them everytime I play the game.

I have a similar problem with custom civilizations. They delete, but will only stay gone until the game restarts. Fix?