First of all, register the employees as per the attendance register in the EPF and ESIC portals. Then, you can file ECR for the pending employees for the pending month(s) under EPF. It will not restrict.
For ESIC, when you proceed, it will display contributions already filed. Opt for supplementary contributions, and from that point, insert the IP number. It will populate the IP details. Enter the number of days and the amount of wages, file the contribution, and generate the payment.