Hi there, HGA.

I understand the convenience of refunding an invoice partially via Merchant services. I'm here to direct you to our representatives for further investigation.

There's an in-progress investigation about the missing processing tools in MSC for Master Admin users in QuickBooks Payments. Please know that our engineers are actively working to prioritize this issue. However, we're unable to give an ETA for resolution at this time.

If your Gopayment app is associated with QuickBooks Desktop, you can chat with us from Monday to Friday, 6 AM to 6 PM PT. Rest assured that our experts will help you figure out why you're unable to process refunds online. You can also call us at the number on this article: Contact Payments Support.

Here's an article as your guide in accepting settlements on the go: Process payments in the GoPayment app

I've added the Record GoPayment transactions if you need to transfer payments from the app to QBO.

Feel free to get back to this thread if you have other concerns with working payments. I'll be right here to help you. Take care!