If we will follow this process you will receive an error most especially if the transaction was electronically done and we don't have a way to modify the amount of the bill payment to the right payable amount.

What I highly suggest is to: 

1. Create a deposit with the amount refunded and changed the account (category) to Accounts payable to offset the initial incorrect amount of the bill and bill payment( see screenshot attached. For proper register recording.

2. Create a vendor credit of the exact amount refunded- this is nonposting so this will not affect your reconciliation or hit your register. This will only offset the vendor's balance. (see screenshot attached)