Gratuity means of continuity in service, this is not related to EPF nor any govt. body; this is purely from the management to the employee for his service.
in your case, if employee have same employee ID or registration details for before and after the re-joiner, gratuity can be count from starting of his job, if not gratuity will count from 2008 on wards.
any mal-practise, include behavior grounds; gratuity will not come for employee with a valid reasons and documents.
But has employee now resigned that question of gratuity has come up.
First of all determine from which period has employee been working continuously and then gratuity amounts can be worked out.
Kindly check all employment records,PF records etc and give an appointment order from that date onwards.
Appointment letter should not be back dated.
Company needs to put in place proper HR policies of appointment and exit.
This will help the company as well as employee and make you legally compliant with labour laws.