To make changes to a pay run you can unlock it to remove the job keeper end date from the employee's payroll. You can do so via the link below:
By making changes to the pay run, you will need to then run an Update Event to update the ATO on the new changes. Please use the link here to see the steps involved in submitting this type of single touch payroll event.
If you are unable to unlock the pay run in to remove the end date, it would be best to to run an ad hoc pay run which will involve backdating pay periods to allow you to submit the job keeper details. In this pay run, you would then add in a FN START DATE for the next period, to send through to the ATO the employee is back on job keeper. To change the start date of the Pay Period please adjust the ending date.
For details on how to run this type of pay run, please use the guide by clicking here for steps. Once you've created this backdated pay run, you can use the same steps above to add, finalise and submit the details to the ATO. If you are unsure with any of these steps please don't hesitate to reach out to our support team by clicking here.
Hope this helps,