Thanks for sharing your concern with us, @robertr-turnofth. I want to make sure you're able to get this sorted out.
The Apple Pay payment will be shown in the Merchant Service Center as a credit card transaction. By canceling the receive payment transaction or reversing the payment in the Merchant Service Center, you can cancel an Apple Pay payment that was made by a customer. This is also mentioned in the article: Frequently asked questions about Apple Pay and QuickBooks.
If you have more questions regarding the Apply Pay and QuickBooks processes, you can always contact our Payments Support Team. They can share more details about this. You can reach them through this link: Contact Payments or Point of Sale Support.
I've added this article to learn more about Apple Pay:
Let me know if there's anything else that you need help with invoice payments. I'll be sure to get back to you.
