To refund an eBay order, access the orders within Shopify.
Choose More Actions → Cancel Order
Next, select Refund Payment
(do not select refund later, doing so will not process the refund to your customer)
Choose whether or not to Restock items
Select the Reason for Cancelation and whether or not to send a notification to the customer
Click Cancel order
Once cancel order is selected, the information will automatically update to the order on eBay and the refund will automatically process.