What Shwez said. This was one of the reasons I added the Card Alter. A tip is: if you want to level up a card and maintain its naked/busty, alter the level 0 card you'll combine it with so you can save cash. (Lower-level cards are cheaper)
After re-reading my reply, I just realized that I was silly for suggesting that, since the naked/busty of the lower level card will never matter because combining two cards will always take the higher level card's naked/busty.
In short, there's no need to alter the lower level card. Just combine them.