If you use QuickBooks to generate recurring invoices or you sometimes enter them manually, a sequence between Service Fusion and QuickBooks will eventually break. When this happens, QuickBooks will assume that the invoice you are trying to send it already exists and will simply return an already existing ID as opposed to creating a brand new invoice.
For example, your Service Fusion invoice sequence is 1001, 1002, etc. You create invoices in Service Fusion and sync them to QuickBooks. You then create recurring templates in QuickBooks and have it generate 15 invoices on the 1st of the month. Your QB invoices are now 1003 through 1015; however, in Service Fusion, the last invoice is still 1002. You now create another invoice in Service Fusion numbered 1003 and try to sync it to QB. QB then responds with an ID that belongs to its own invoice number 1003 because it "thinks" that it is the same invoice.
To avoid this conflict, you should set the "When syncing invoices, would you like QuickBooks to assign its own invoice number?" to Yes and also make sure that the "Custom transaction numbers" setting is set to No in QuickBooks.
To turn this feature off, click on the gear icon in the upper right. Then proceed to Account & Settings and select the Sales tab on the left.
In Service Fusion you will see both the Service Fusion and the QuickBooks invoice numbers ion the invoice view screen.