Dear Candidate, 

You need not worry about this. Simply, go to your university and talk about this matter. They will be giving you a paper, get it signed and submit it to GPAT. After that you will be given a stipulated date to clear your backlogs. If you successfully clear your backlog, you will be a part of the counselling. So, you need not worry, you can clear your backlog and be ready for the counselling!

Wish you all the luck!