Money given to us by jk pmsss is only for the maintenance allowance which can be used to pay hostel fees if a student is staying in a college hostel, it can be used to pay house rent if the student is staying in PG. Maintenance allowance can also be used to pay the examination or university fees.
Thus if anything is left from it can be used to pay the Partial admission fees as per the rules of JOSAA. But at the time of admission, you have to pay on your own, and later if something is left from the maintenance allowance you can use it.
The money is not refunded back but is used later as an academic fee so for example if the academic fees if 80,000 then 40,000 is already paid by you and now you have to pay only 40,000. Since academic fees are paid by AICTE directly in the college account you can claim the refund by writing them a letter.
Conclusion: There is no special privilege given to pmsss students apart from the normal structure of fee distribution as per AICTE for the students studying under NIT, IIT, or any other college.