Due to the ongoing hmrc problem i have to submit my vat the old way. Does that mean the quarter will not be locked and late invoices will not be highlighted?

Hello laura42,

If you do not file the return directly through QuickBooks you can mark the return as filed by going to Prepare return > Drop-down beside 'Submit to HMRC' > Mark return as filed. This will lock the period and highlight late invoices as exceptions against your new open return. 

Thanks