Hi Deepak,
You will have to do the configuration change at the start of every month or restrict using IT0003 for all employees at the start of every month.
But this is not a good practice. I assume that your time data goes to some payroll system. What if some time master data gets changed after payroll has been rune? Won't you be sending this data to payroll system?
Thanks and regards,
Vivek Barnwal