Does Apple Pay support refunds?

Refunds can be processed on Apple Pay transactions.
There are two methods that can be used to do this:

Using Webservices API
Your server can submit a new REFUND request to Trust Payments in order to process a refund. Refer to the following documents to learn more:

Using MyST
You can sign into our online transaction management portal MyST in order to process a refund. You will need to search for the transaction that you would like to refund and click the Refund button displayed on screen.