Ravenous16th,
this is because the 'available' ship designs are stored in the save game file. And these 'available' designs are added to it either (in the current game) by designing a ship during game-play or during game creation by scanning the design folder.
Adding designs to the directory will not make them available in already existing game(save)s, because the design folder is not rescanned during an active game or during a game load.
In one of the dev feeds Paul said that they might think about making a 'import' button in the designer to actively load a ship design / part design.
The same happens with the xml files and possible other resources too.
I have requested a feature to allow the in-game updating of xml files for modding and testing, but maybe a similar feature could be requested for ship designers and the (test) users of these designs.