When the Invoice was synced into Sage 100 we found that another posted invoice with the same invoice number and vendor coding already exists.  

You should confirm that the invoice is in fact a duplicate invoice. If you find that this is the case, you can simply "Mark the Invoice as Exported" in Beanworks. Since the data already exists in Sage, you don't need to export it again.

It's possible that the invoice is in fact a different invoice, this sometimes happens with vendors who 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 sync into Sage.