According to HMRC guidance when you process your pay,the pay period which the employee belongs to is not the criteria for calculating the Employer Payment Record (EPR) amount due. EPR is consolidated based on the payment date you entered while efiling FPS returns. If the payment date belongs to a different tax month then the amount due will be reflected in the EPR for that particular tax month.

In this scenario you may find your employees belonging to a certain pay period have gone missing from that pay period. This is because they have been consolidated EPR for the PAYMENT DATE tax month and not the pay period end date month.