Hi
I would run a separate pay run for this employee. When starting the payroll, choose 'Process all employees paid: Bonus/Commission" - as this will clear out any standard pay element and provide a 'blank' payslip.
You'll need to manually calculate the super due from the employees pays. Then put the unpaid Super amount in Superannuation Guarantee at the bottom of the payslip, and continue processing until recorded.
I would personally choose 'Pay Slip Delivery Status: Already Printed or Sent' so that the employee doesn't get a $0 payslip (but you can opt to send this to the employee as proof that you've fixed the Super issue).
Hope that helps/makes sense :)
vidario