Overpayment in ACH and now a credit has been issued

@MMM1107 

Just so I understand, you received payment in full on the invoice and then reduced the amount of the invoice, thereby leaving the difference as an overpayment, correct?  Then, you also issued a credit memo for the same amount?   If I'm not understanding that correctly, please advise. 

If I'm understanding that correctly, then the reduction of the invoice amount and the issuing of the credit memo are duplicate entries.  The proper way to handle that should have been to leave the invoice at its original amount and issue a separate credit memo.  At this point, you can change the invoice back to the original amount (make sure the payment is applied in full) and leave the credit memo as the credit.  

No, I sent a revised invoice, but they paid the original amount.  So I have nowhere to apply the dollar amount when I am matching in bank transactions.  I did issue a credit, but I don't know where to put the money that was overpaid in the bank transactions.

@MMM1107 

"So I have nowhere to apply the dollar amount when I am matching in bank transactions. I did issue a credit, but I don't know where to put the money that was overpaid in the bank transactions."

For the sake of argument, let's assume the original invoice was $1,000, the revised invoice was $800, and the customer paid $1,000 via ACH.  When you received payment on the invoice, did you use New > Receive payment and enter $1,000 in the 'Amount received' box?  If so, then you should have a $1,000 payment to match with your bank feed and a $200 A/R credit for the customer.  Since you mentioned "I don't know where to put the money that was overpaid in the bank transactions.", did you only receive $800 on the invoice?  If so, change the amount on the payment received to $1,000 and delete the credit memo.