Full-priced goods purchased via Afterpay are still eligible for a credit note or an exchange, however, your original payment schedule with Afterpay will continue until payments are completed. Visit the Afterpay site here for their terms & conditions.
If you are exchanging for a more expensive item, the customer service team will offer a credit note that way you can use that to purchase the new item and the customer initiates the extra payment in a safe method and provides the correct invoice.