How do I record an Admin AP refund so that the vendor 1099 is correct?

You will first need to process a non-gift to record the refund, debiting the appropriate asset account and crediting the appropriate expense account(s).

In Accounts Payable:

• Go to the Vendor Tab and select the Vendor ID
• On the top right of the screen click on the field labeled 1099 Adjustment
• Enter the amount of the refund preceded by a minus sign.  This will deduct the refund amount from the 1099 amount
• Enter the details of the refund in the Description field.
• Save

Note: This assumes that the 1099 Adjustment field was cleared after last year's 1099s were run. Also, there may be additional adjustments to the current year's 1099 due to various factors. If so, the adjustment amount will need to equal the sum of all the adjustments for the year. For example, if there was an adjustment of -100 in January and +200 in June, the adjustment amount should ultimately equal +100.