If you see the screen below -- "Order already refunded" -- you will need to close out of the window by clicking "Continue" and adjust the Refund Due amount accordingly.
This occurs when a partial refund has been issued directly within Shopify after order placement.
After clicking "Continue" you will see the RMA has transitioned to a Pending Refund status, which is covered in the linked help center article. For example, in this case, you would reduce the amount by $1.11 using the Deduction & Fees field before clicking the Process Refund button.
As a best practice, it's ideal to avoid issuing partial refunds for discounts not initially applied at checkout for a corresponding order. When partial refunds are issued on Shopify, these amounts cannot be attributed to a specific product from the order. For example, if an order was placed for five items, and only one is being returned.
We certainly recognize the use case for issuing such partial refunds, and the importance of maintaining a positive customer experience. However certain limitations necessitate differing approaches to such circumstances when returning.
In these instances, shoppers are still able to successfully initiate a return and where a reflected Refund Due amount cannot be fully allocated (due to exceeding the available refund potential), messaging is triggered indicating such and Returnly prevents an over-refund scenario.
