Apply Credit Memo - Cannot exceed original invoice balance

We have created a credit memo to a customer. When the order was entered, a deposit via credit card was taken. When the order shipped, the system created the invoice and charged the credit card for the balance due. The credit is for more than the deposit or shipment invoices individually. So when I select the credit card transaction I’m not able to change the amount of the sale to be more that either of the invoices. Do I have to do two “apply credit memo’s”?

If you have a credit memo for $400 and an invoice for $100, you can apply that credit memo, but you have to enter the proper amount to apply of only $100. It will default to apply the full $400 though.