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Customer refund unlinked from payment

Could I please ask for some help here. We have a customer refund that has been for some reason unlinked from a payment batch / payment but it was still paid out through the bank to the customer. The AR seems to be correct as the customer record shows $0 balance on the customer but the Global payments module still show this customer as payable for refunds.

I looked at the System Notes for the refund record and there were a couple of changes made to the record after the PFA was generated. Including payment method being set to EFT and cheque number being removed. Could this have caused it to unlink? I'm thinking setting the payment to EFT after the payment file was generated could be the issue?

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