Yes youvcan surely attend Counselling at Thapar college, but you shall be allotted seats in basis of whatever is available at that time and not by your preference. 

You should also write an apology letter stating reason for not attending to avoid any hassles at tim eof admission. 

For Josaa Counselling you can check below details. 

https://engineering.careers360.com/articles/jee-main-counselling-seat-allotment