I'm having a similar problem but we are now finding Invoices that we processed through QB Desktop Pro 2019 that have marked as Paid showing up 5 months later in our to be deposited list that were never actually processed and I'm having to call customers and try and re-run their cards for large amounts.  I'm afraid of how many more are going to just show up out of nowhere and how much money is sitting in limbo. Can QB audit our account file against merchant service transactions and find out. If not we are going to go with a different merchant processor and start doing it manually again.