Total Gross recorded by us and by ATO does not agree. Problem identified but need an immediate fix!

I was using Payroll Premier 2018-2019. At the beginning of November 2018 I had a problem with the ATO not recognising the Product Number through the Portal. Following on from this I had telephone support and advice to change the product number even though we had not changed the product or updated the software so that all STP reports following on from this would lodge successfully, which they have. I was advised that if the total ytd gross was correct in future reports, then there will not be any problems.  WRONG!!  The ATO data is showing that the data submitted prior to the change of product number in the system is a separate entity and doubling up on the income and tax paid.  What do I do?  Urgent