For merchants leveraging the Gift Card API, only available on a Shopify Plus plan, to issue refunds to a gift card there are times when a customer requests a refund back to their original form of payment. In order to avoid over-refunding the customer with both a gift card and a refund back to their original form of payment you can take the following actions.
Disabling the gift card
Within Shopify you will navigate to Products > Gift Cards and locating the gift card ending in the 4 digits listed on the RMA detailed view, as seen below.
Once you have located the gift card ending in the 4 digits provided within Products > Gift Cards in Shopify, you will want to select Disable, as seen in the screenshot below.
Once the gift card is Disabled in Shopify it will no longer be available for use by the customer. You can then issue the value on the gift card back to the original order within Shopify knowing that the customer will not be over-refunded for their return.