When some payroll has been processed incorrectly for an employee and the RTI has already been submitted, you will need to give a reason to HMRC for any RTI re-submissions. This is only required if you have passed the payment date for the employee or employees. There maybe a requirement to bulk un-process and reprocess the employees if you have already imported into accounts.
Navigate to Payroll > RTI > File FPS.
The reprocessed employees will appear in the RTI 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 made an RTI submission before the payment date, you are not likely to get a fine for this. However, if there was no submission made for RTI 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.