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I don't see a problem here, if buyer had already bought single product from collection and he feels that he should be discounted for that, he can always use make offer button. Also there is possibility to contact with seller directly and explain situation. It's not turbosquid where everybody are isolated from each other. Here communication is encouraged and good communication can solve almost any problems.
I certainly wouldn't want that system automatically would adjust price of my collections, no matter what reasons. I think such cases are rare enough to be handled manually without much trouble.
