Follow the instructions in the Refunds Dialog and Manual Refund Dialog screens, entering the payment amount if prompted. The options offered will depend on the refund method, either manual or automatic.
Notes
?"Automatic" should be selected if the Credit Note has been generated from a Return or Refund or if the payment is by cheque, cash or credit card (and credit card integration is installed on the system).
?"Manual" should be selected if the credit note has been manually raised or a PDQ machine is used to process credit cards, or if the payment was originally a Shopify payment. You'll need to refund the payment on Shopify too.