First, you need to issue a credit invoice for the core so as to remove the core from the list of outstanding cores for this customer.  Make sure the terms are 'Charge' so that this invoice will result in a Credit entry to Accounts Receivable for this customer.

Using Transaction | Receivable | Ledger create an entry to remove this item from Accounts Receivable.  This would include a Debit to Accounts Receivable for the amount owed to the customer, and a Credit to a Contra account for the same amount.  A Contra account is a GL Account called 'Contra', that is used to move transactions between ledgers.  If you don't have one, create it before you do this entry.  Don't forget to post the entry after you have input it.

Using Transaction | Payable | Ledger create a Payables entry for this customer.  If this customer does not have a payables account, you could use the 'Occasional Vendor" account.  Credit Accounts payable for the amount owed to this customer and Debit the Contra account.  Don't forget to post this entry.

Now using Transaction | Payable | Payments issue a payment for the amount as posted in the previous entry.