You'll need to contact HMRC first to verify the status of your VAT return. If it's rejected from their end, then follow these steps to change the filing status to Filed.
From the left menu, go to Taxes.
Look for the rejected VAT filing that you need to change and select Resubmit return on the right of the file.
Choose Mark as Filed from the drop-down menu.
If the submission went through, then I recommend reaching out to our QuickBooks Support Team. They'll be able to help change the status in your account with more tools.