In general there is no specific treatment now for EC sales vs sales to the rest of the world. Where applicable (depending on the place of supply rules) sales invoices to EC based customers should instead be zero rated. The client level EC flags will be removed in April, but remain for the time while invoices are still being input for the period before 1st January.
We will be releasing a bulk update tool to remove all EC flags in the coming days. We will also be extending the bank tagging section to allow these new VAT provisions to be applied there too. Further updates will follow.