There isn't a lot you can do right now except write to them (certified, return receipt requested) and explain, once again, that until proven otherwise, you believe that payment always cleared before shipment. Try to resolve this amicably.
If you're unsuccessful, you can't really do anything to keep them from taking this to a collection agency. But after the collection agency contacts you, you can send them the same letter, also certified/return receipt.
Finally, they could take you to court. But they would have to prove their case, and if you win, you'd be entitled to attorneys' fees and costs if that's what your written contract with them says (you do have a written contract, don't you?).
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