STP Payment after final event

We have processed a final event for employees that left last year who had salary sacrifice arrangments in place.  A final event was submitted on their last pay. 

The Salary sacrifice provider has now advised that there has been an overpayment and we need to refund the employee.  The values are small so no PAYG involved, but because these have to go through payroll again we have to reactivate the employees

Will this cause an issue with STP and then do we have to do a final event again after the payment?

Or is there an easier way to do these?