You've received this error as there is an invoice in your Quickbooks Desktop with the same combination of Invoice Number and Vendor. The error is to flag this invoice as a possible duplicate.
You should confirm that the invoice is in fact a duplicate invoice. If you find the invoice in QB is the same invoice, you can simply "Mark the Invoice as Exported" in Beanworks. Since the data is already in QB, you don't need to export it again.
It's possible that the invoice is actually a different invoice, this sometimes happens with vendors that are poor at using unique invoice numbers.
In this scenario you should Reset the invoice in Beanworks and amend the invoice number to something unique. Once you export and sync the invoice again the invoice will populate in Quickbooks as it no longer views it as a duplicate.
A little advice:
If you have a few worst offender vendors when it comes to invoice numbering or don't provide an invoice number at all. Make a practice of changing the invoice number in the coding phase.
For example: I've a vendor that doesn't send me an invoice number but rather a customer number which is the same on every invoice I receive from them. I could use the customer number plus the date when coding the invoice number to make it unique i.e. customer number: 200392 becomes invoice number: 200392-MMYY. This way you'll cut down on the amount of possible sync errors.
It's important if you introduce this policy that you're entire coding team are following the same process. If not strictly followed a real duplicate could slip through the cracks.