I considered reversing the transaction.

But we do not want to do this, because the 2nd payment really did flow out of the bank.
Our Bank Statement shows the payment happening twice.
We want to leave the two payments as is, since they really did happen.

Rather, we want to show a deposit from the Vendor, indicating that they made a payment to us.
And of course, to get their account in balance, not displaying a credit balance.