Thanks for posting your question here in the Community. I'd be happy to help get this taken care of today.
Since you're using a third-party application to download invoices to QuickBooks Online (QBO), I recommend contacting them so they can help you look for ways preventing these duplicates occur in the future.
In the meantime, let me walk you through deleting those duplicate invoices manually in QBO.
On the left pane, select Sales.
Select the All Sales tab.
Select the Filter drop-down.
From the Type drop-down, choose Invoice, then select Apply.