When some payroll has been processed incorrectly for an employee and the FPS has already been submitted, you will need to give a reason to HMRC for any FPS re-submissions. This is only required if you have passed the payment date for the employee or employees. 

The reprocessed employees will appear in the FPS submission. Towards the bottom, there will be a drop down which will require you to give a reason for the late submission. Please choose the most appropriate reason and then click on the Send to HMRC button.

Please note: this drop down box will only appear if there is a submission made after the payment date. If you have submitted an FPS before the payment date, you are not likely to get a fine for this. However, if there was no submission made for FPS and the payment date has passed, you will need to give a reason and you may still get fined. Please use this link to get further information on the fines given by HMRC for late submissions.