Calling a client to get their credit card number when a partial return is required is a pain. Please allow for partial returns on invoiced items. Quickbooks and Paypal both have this feature as a standard feature.
Great news, MX Merchant has this feature as well! There are two different ways to perform a partial return in MX Merchant without needing to reach back out to the customer for their card number. You can make a return on the original payment or you can return an item which will return the proper amount back to the original payment method.
For more information on how to make a partial return on an invoice, I've included screenshots below for both options. The Blue help text shows you for a basic refund, and the orange help text in the screenshot shows you how to do an item return and refund.
Hope that helps!