Here is my response to this common problem:

Attaching a bill to a payment after reconciliation (DESKTOP)

The need for this procedure arises when a payment has been entered and reconciled before it is attached to a bill. The payment is reconciled but the bill is not so the bill persists in the Pay Bills list after the corresponding payment has been entered. The bill appear unders “Home > Pay Bills.” The payment appears under the vendor’s name under “Vendor Information”

1. Open the payment (either Cheque or Credit Card charge).
2. Change the Account to “Accounts Payable” and enter the Vendor’s name under Customer/Job.
3. Change the TAX to no tax (E) and Amount to the total amount. Save and close.
4. Open “Home > Pay Bills” and scroll to the Vendor name. Check the box to the left. (The Vendor name must be in the list because the bill is unreconciled.)  
5. Select the vendor (Click the box) and Choose “Set Credits” (third button below).
6. In the Set Credits box, choose the credit item created in steps 2 and 3 above. And click “Done”
7. Ensure the Vendor name line is selected and the check box checked. Click “Pay Selected Bills”.
8. Under Home > Vendor Information <the vendor> check that the payment (Check of Credit Card Charge) is “CLEARED” and that the bills are “PAID”.