If you have invoices still in your list that are already in QuickBooks (due to the recent server migration), you will want to close those invoices out without them being sent to QuickBooks a second time.
To do so, first navigate to the Invoices > Pending Invoices page.
From here, access the drop-down menu and select 'Bulk Close Invoices'.
Select the date range, whether to target only 'zero dollar' invoices, and the Status you want to target, then click 'Submit'.
Those invoices will move from the Pending Invoices page to the Closed Invoices page without being sent to QuickBooks.