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Hi there, @CarynG,
You can open the deposit and set the accounts payable under the name of your vendor to offset the overpayment. This process will link the refund and will surely close the credit amount.
I’ve attached an article in case you need a reference: How do I handle vendor credits and refunds?.
Please let me know if you need further assistance on how to offset your vendor’s overpayment. I'll be on a look out for your response. Have a great day!