My VAT submission has been confirmed by HMRC but quickbooks is saying the return is open. Do i ignore the message box?

Good day, @accounts48,

You'll be glad to know that you can mark your VAT return as filed in QuickBooks Online.

Let me guide you through on how to accomplish this:

1. Select Taxes from the left menu.
2. Go to the Return tab.
3. Select the VAT return, then click Submit Return under the Action column. 
4. Click the arrow down beside Submit to HMRC, then select Mark as filed. 
5. Click Continue on the All done? window to confirm the message.

If you've already paid your VAT, then you can record your payment.

Please read through this article for your guidance with the solution above: Submit a VAT return in QuickBooks.

Let me know if there's anything I can help you with filing your return in QuickBooks. Just leave a commend below and I'll get back to you.