Dear Shilpi,
How are the two connected?
You can have 2 set of employee codes, but is it not increasing your burden only. You have to maintain the data in multiply sheets and thus you are opening a gap of mistakes to happen.
You can by mistake, give the Bio Meteric no. to someone else in the PF and thus, the PF can be transferred to some other account. You are starting confusion and more work for your own self.
It is advisable, that the person's emp code, bio metric code, PF no all be the same to avoid confusion and mistakes while preparing reports and payments.
Regards,