Dear Prijith,
First of all, why are you accepting any change of shift without any intimation to the HOD or HR? This should be treated as late coming or early going as per the shift schedule assigned to the associate. You can deduct salary for late coming/early going, and after deduction, you may also issue a warning letter for late coming/early going. However, the only necessity will be for the HOD to relieve the associate as per the scheduled shift time.