Went back and forth for 2.5 hrs today between QBO and Payments.  QBO -> Payments -> QBO -> Payments.  Francis took responsibility and walked through the process again to see and acknowledge the discrepancy and did a personal handoff to payments.  Payments did a lookup knowing there was an existing investigation (INV-101657) and stated that our workaround of processing copies was all we can do for now.  We're suppose to be updated via the investigation and were told that dev is aware and working on a solution.