Any CC that is on a sim in the Gallery will not be passed through to your game. For example, I downloaded a sim that was heavily done in CC, hair, and clothing, when I downloaded them, the sim was bald, and in their underwear.
Now as far as sims showing up as duplicates in the gallery, don't delete the duplicates. I did that once, and when my library sorted itself out, I ended up losing several sims. I'm not sure what causes it, but there are times I will see several duplicates, but then later something gets corrected, and I am seeing the one sim, instead of two.
