1. Void and purge the check for the duplicate invoice from the invoice.
  2. Delete the duplicate invoice
  3. In General Ledger, Journal Entry, re-enter the check paid to the vendor
  4. Record the deposit through a manual Journal Entry in General Ledger
  5. Post the deposit to the same date as the Journal Entry check, effectively canceling out the original payment

The General Ledger will now match the actual events of the scenario without a credit memo. There will not longer be a record of the duplicate paid check, invoice or refund in Accounts Payable, but the General Ledger will match these steps and effectively cancel out what should have not occurred.