Hello dkjones, 

You'll have to create an ad-hoc pay run for this to record the back pay of the employee. Since there is a super payment on the affected pay run, we're unable to unlock the pay run.

Creating an ad-hoc pay run is just like creating a new pay run in QuickBooks Online Payroll. Click on the Employees tab, and click on New pay run. Make sure to select the same details that the original pay run has like the pay date and ending pay period.

Once you have created the ad-hoc pay run finalise the pay run and lodge them to the ATO.

You can also check this article to learn more about How to create an ad hoc or off cycle pay run in QuickBooks Online Payroll.

The Community is here to help you if you have more questions about QuickBooks Online. Have a great day!