How do I process returns with Apple Pay?

Use the Device Account Number to find the purchase and process the return, just like you would with a traditional credit, debit, Suica, or prepaid card payment. In Japan, you can also use the transaction ID on the receipt to find the purchase and process the return.
To see the last four digits of the Device Account Number, ask the customer to go to Wallet, tap the card, and tap  on the lower-right corner of the display.
You can also have the customer hold their iPhone or Apple Watch near the reader, select the card that they used to make the original payment, and authorize the return with Face ID, Touch ID, or a passcode.

To process returns with Apple Pay you need to send Service API request as for usual Credit Card transaction.

https://support.apple.com/en-us/ht204274

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