To issue a refund for a payment taken in the Scratch Desktop App:

Create and post a new invoice in your Cornerstone dashboard
Enter the refund amount in the Amount field as a negative number. For example, if a $10 charge was refunded, type -10 in the Amount field. Then, choose Scratch Payment as the Payment type.
Click Post and then Close.
Select the payment notification on the bottom right of the screen to go to the Scratch Pay desktop app.
Click on the line item of the invoice for which you would like to process a refund.
Select which payment to refund from the right side panel.
Click Process Refund.
The refund will be processed.

Cornerstone / Scratch Checkout Integration User Guide

Processing payments directly from Cornerstone using the Scratch Checkout desktop app