I have just tried it I now understand what you are saying.
I just made a version 2 of a ship, and it obsoleted the first version - which I still wanted to keep around as an option to build.
I agree - this should not occur. It is impossible to use a consistent template throughout the game and keep the different versions. Big Problem. Kills much of the fun of the Shipbulder.
Is this a bug or feature? If it is a feature, can we have the option to turn it off? TIA!