This issue started for us  14 months ago. It happened for only 1 customer.   All Invoice Numbers have been the same for that whole time.   The poor customer suffered in silence all those months.  I feel sorry I didn't notice it before last month.   Invoice Numbers were fine before 14 months ago.   14 Months ago may have been when we enabled this as a scheduled monthly recurring transaction.   The number QBO seems to have chosen is the same number as an Invoice number for an Inactive Customer from 2006 (coincidence? - probably). 

I Deleted the latest invoice with the bad number and Used the Recurring Transaction to recreate it and it received a new Invoice Number.  I have no idea what will happen automatically next month.

Adding Duplicate Invoice Number Warning capability to QBO like the other Duplicate warnings would have caught this software problem instantly .