Hi Kinpel97,
Thank you for your post.
First, what you should have done is to zero out your pay history and finalize your payroll with the old ABN before changing to the new ABN. This is to ensure that by the end of the payroll year, employees will have only one income statement from their MYGov. In this case, since it has doubled up the figures reported to the ATO, I would recommend contacting the ATO to inform them that you’re using a new ABN for your company file and no longer using the old ABN. You’ll also need to inform them that you’re unable to finalize your old ABN payroll reports.
Please let me know if you require any further assistance. I'm happy to help.
Cheers,
Princess