I was using the ship designer from main menu to design ships.
I made a ship design, but I later decided to change it. I wanted to use the same name, so the game asked me if I wanted to overwrite the file. I said yes and everything seemed fine. The designer showed the ship and its equipment had been changed to the new design.
However, I later couldn't find the ship in the ship designer. I had exited the ship designer and went back in. The ship was gone. I then exited the program and restarted (to see if that changed anything), but the ship design was gone.
I opened my save folder and I could see the files for the ship design in question. I then tried to make another ship with the same name, and it apparently overwrote the ship without asking me if I wanted to overwrite. I then could see the ship design after exiting the designer, and after exiting the program.
My conclusion is there is something broken for overwriting ship designs.