Im new to QB and im uploading all invoices and a couple of invoices has already been filed in previous VAT return but QB wants to account for it again??

Welcome and thank you for choosing QuickBooks, @marc22.

Allow me to ease your confusion regarding your uploaded invoices.

The possible reason why QuickBooks prompts you to account for the already filed invoices in the previous VAT return is that you uploaded transactions prior to the filed dates. This will also add to your current VAT return that results in inaccurate data.

To ensure your VAT return is accurate, you'll want to unfile it and mark the return as filed without submitting anything to the HMRC. You'll have to do this until you reach the current period of the VAT return that shows the correct data.

However, unfiling VAT return requires pulling up your account, which our QuickBooks Support Team can do. That said, I suggest reaching out to them to help you unfile the return and correct it.

I'm also adding this article for your future reference on submitting a VAT return: Submit a VAT return in QuickBooks.

Please let me know if you need clarification about VAT returns, or there's anything else I can do for you. I'll be standing by for your response. Have a great day.