When you post a credit-memo, you will anyway affect two accounts (as it is a principle of accounting). In the header of the credit memo you will select a customer, and this would be your receivables account that will be adjusted by your credit-memo. However to post it, you need the other side of the accounting transaction, which will come from the lines of the credit-memo. Now, in the lines you can select either items (so that items quantity and items value will be adjusted), or G/L account, so that only some G/L account will be adjusted, but not inventory.
Regarding your comment of the new system: if your customer has been invoiced in old system, this means that you had a transaction of Debit of receivables account and Credit of Revenue account. While going to new NAV system, you most likely transferred the Revenue account as well (or, if it has gone to previous periods, now it is Retained Earnings in NAV).
So, in order to reduce customer's balance at current date, you need also to select Revenue G/L account in your new NAV system.