I recently noticed (in 1.5 stock) that when a ship undergoes a 'refit' (i.e., you get a screen in port saying that you got a new conning tower or whatever), that all of the previous ship upgrades are lost. This might be a bug, but it's a bit annoying. My Salmon class ship recently got a new conning tower, and I lost my air radar, my 4.50 deck gun, my twin AA guns, and my surface radar.