Hi HappyFeat,
Thank you for the post. I understand how important it is to ensure that everything is reported correctly. Here's quick and straightforward way to resolve this without re-running 52 pay runs.
First, go into your payroll settings and change the deduction type of the affected employees to the correct reporting category as required for STP Phase 2. After updating the reporting categories, send an update event through STP to the ATO. This will ensure that the corrections are reflected accurately in the records.
Regards,
Sai