An update has been released to resolve this error.
From the AccountEdge menu select Check for Updates.
Click Install Update and follow the prompts.
You will need to run the payment summary assistant again to recreate the EMPDUPE file. You will then be able to submit the EMPDUPE to the ATO.
Already closed your payroll year? After installing the update, you'll need to restore the backup you created prior to closing the payroll year. You can the recreate and submit your EMPDUPE file.