Lodge BAS for a new period ,skipping a Due BAS form a previous period???
The GST centre within QuickBooks works to update the ATO not vice versa. If your accountant has already lodged your BAS directly with the ATO, to ensure continuity of your books and figures within QuickBooks it would be best to lodge the BAS period also. Whilst there is an option to lodge directly to the ATO from QuickBooks through Electronic Lodgment you have the option to only lodge in QuickBooks instead, and you do not have to lodge it with the ATO.