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Hi there, keating.jan.
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You can create a new pay schedule called Ad Hoc/ adjustment pay run to record the employee's unpaid amount. This separate pay schedule stands out from the other regular processed pay runs on your Pay Runs tab.
Then, the PAYG and Super will also be calculated base on the remaining hours/total gross in addition to the underpayment.
You can check out the How to create an Ad hoc pay run article for the steps and details.
Once done, create an update event and lodge it to ATO to update the lodgement. For the steps and details, you can check out this article: Create and lodge an update pay event.
I have articles here about managing Pay Run:
Please reply to this post by adding some details below if you need anything else with running payroll. I'm here to help.
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