How to record reissuance of check from third party (Avid Exchange) refund to not overstate 1099 vendor totals

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My company uses Avid Exchange to cut checks. We have a check that got outstanding for too long and Avid refunded us the money. How do I reissue the check without overstating the vendor totals for 1099 reporting purposes. Here are the problems I came across while trying to find a way to do this:

1. The initial invoice has been paid and cleared in Cash Management since Avid actually takes out the money from our bank regardless of if the check remains outstanding later on. Therefore, I cannot void the initial check that got refunded and pay it again.

2. If I record the refund in Cash Management as a deposit credit to an exchange account that will be reversed by "re-entering" the invoice again to reissue the check, the vendor totals will be overstated since the amount of the invoice will show up twice in the 1099 report.

3. I cannot treat the refund as a credit memo (entering a negative invoice) since I have to reissue the payment. I can't think of a way to clear the negative amount in the aging because doing a zero check payment is I think impossible when I have to cut a payment again.

This is the first time I came across with this issue so I am having a hard time wrapping my head around it. Any help would be appreciated. Thanks!