If an Integration is not sending invoice numbers to QB – it is reading them from QB after it is created. So with your setup (QB Ref Number is generated in QB) it cannot fix the issue. The change to Invoice number sequence could happen only if somebody manually created an invoice with a new sequence start number. For example if your last Invoice Number was 2033 and I create an invoice manually and assign a number 2033-1 – QB will generate next invoice number as 2033-2, 2033-3 etc. More of it – if your last invoice number was 4789 and you create manually the invoice 2033-1 – QB will continue generating for next invoices 2033-2, 2033-3 etc. More dangerous situation – if you had a gap in invoice numbers like 11, 13, 14 ,15 etc. and decided to create invoice #12 – QB will continue generate numbers for next invoices as 13, 14 ,15 etc. so you’ll have duplicate numbers, which is very dangerous if integration is running. Long and short:
 
  1. Never create Invoices manually with numbers that can reset number generator or (if it is critical) always manually reset generator back (see #2 below).
  2. To reset number generator back you need manually create an invoice with the number you want to continue with. For example – if the last invoice was #2033 – create the one with #2034. If it was 4789 – use 4790. Updating existing invoices will not help! You can delete that dummy invoice after integration creates next invoice with a correct number.

Please instruct everybody who can manually create invoices regarding this issue.