Can I change branch preference after first counselling at Thapar University?

You should not worry as you will get a chance to get your desired branch at the time of In-person Counseling. 

When you attend the In-person counseling, you will be allotted a fresh paper to fill up your choices, and then you can change as per your choice or interest. Till that time, you will have to retain your allotted seat. 

You should relax as you have been allotted a branch at Thapar University. You can change your branch in later counseling. It is important to have patience and be updated with the counseling dates.