Why are you giving them a deck with a duplicate in it? That's just stupid. Palm it out or don't let them see the deck.
There's nothing wrong with giving them a deck with a duplicate if that's not what they're looking for. Chances are very high that it will go unnoticed. If the duplicates are side-by-side in the deck, then it'd be noticed & raise suspicion. But, let's say you're doing an ambitious card routine with a signed card. Some people might want to observe the deck for some reason (as pointless as that would be). Would they be looking for a pair of duplicates in the deck? No. They might be curious to see if there is another signed version of their card or something. And even if they did find a set of duplicates, it wouldn't have anything to do with how you made a different, signed card keep going to the top of the deck. And if they ask about it, you can just say, "Oh, thanks, how'd that get in there?" Or, "That's where that card went! I was missing it from another decck." There are many other things you could say. But, again, chances are very low of their finding duplicates in the deck.