I concur. I have a few of those 0 dollar CCU's in waiting for just these reasons. I want to play with the Reclaimer when she comes out, and then turn her back into my Carrack. It just makes sense to use the ship that is flyable, then switch to the ship you want later, when shes available. The ship itself is wrapped up in a Mega Explorers pack, so melting every time isn't an option. Same with my Redeemer to BMM CCU. I was going to apply that girl when the time was right.
Now I need to decide, definitively, what ships I want RIGHT NOW, before they start erasing my saved CCU's. That's fucking balls.
Also, yes, methinks they hate the fact that people got "cheaper" ships. I've upgraded many ships this way. *shrug* Oh well.