This issue is ongoing. I use Quickbooks Desktop Enterprise and regularly send invoices via email with the option to pay via ACH. If the customer makes a partial payment as opposed to a full payment the link and that invoice is essentially broken permanently regardless of how the payment is recorded. I've added the payment from the merchant center, and recorded it manually. The workaround I use for customers that want to make multiple ACH/CC payments is to duplicate the invoice, move the previous payments to the new invoice, and then create a balancing credit against the original invoice. This is time consuming, a recording nightmare of a mess, and extremely frustrating for me on top of being confusing and unprofessional for customers to deal with. This is not a user error, it is a technical error I desperately wish Intuit would resolve.