To enter a credit on a credit card (or for that matter a bounced check from a customer)...
Create a new cash batch.
Enter a cash transaction to the customer and enter a negative dollar amount - the amount of the credit.
Use as the check number the same number you originally used but change it slightly - put a CN as a suffix, for example.
When you get to the details section, highlight the original invoice (which probably has a zero balance) and apply the negative amount to the invoice, bringing the balance back UP to its original amount.
Save and post.
This will debit AR and credit Cash, and increase the balance due from the customer in AR.
At this point, if it turns out that the invoice also needs to be credited, you can then credit the invoice in the normal manner.