Hello Rohit,

Generally, If a student is called for counselling and student gives a registration fees. If you do not get admitted in a college, your registration fees is NOT refunded. Also according to JIPMER official website the fee is NON-REFUNDABLE. 

More - https://medicine.careers360.com/articles/jipmer-counselling

Hope that helps and feel free to ask if you have any more queries. Best of luck!