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Vendor Payment paid by EFT to be refunded what about the 1099?

edited Dec 23, 2019 10:48PM in Accounting / ERP 1 comment

We made a vendor payment to a vendor that is 1099 eligible. Part of the payment was reimbursed expenses and part was contract fees.  This Vendor received the payment in his bank account but is now issuing us a check in the amount of his payment so we can reissue correctly. How should I handle this when I can't void the EFT payment in the system since the cash was deposited into his account?
As it stands now he will be sent a 1099 that includes the money we were reimbursing him for expenses. 

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