My friend made a 1:1 DVD Backup of Soul Calibur 2. He used the swap magic discs with his flip top cover, but could not get it to boot. The Swap Magic indicates that the disc is fine, but when its supposed to boot, it does not. Is there anything that can be done to get it to work?

yeah, use cd loader to load the game as swap magic alone won't work with sc2, and as far as cd loader goes, if you look at the top thread on this page it will answer all your questions about cdloader if you have any.