You’ll notice that there is no option to delete a pay run if you have already submitted STP for it.
However, there is a way to remove these values.
Follow the steps you would take if you were editing a pay run.
When you’re in the Adjust section, make all of the values 0.
Check in Review that all of the values are zero (tax, pay and super).
Submit and report STP with this update.
Now, the ATO won’t register any values for this pay period.