Chotrani controlled the rallies and capitalised on the mistakes of Baitha to win 11-6 11-8 11-9 and move into the last eight of the tournament being held at the NSCI courts.
Top seed Tushar Shahani of Maharashtra defeated Abdur Rehman of Delhi 11-9 11-7 8-11 11-5 to book his place in the quarter-finals.
In the under 15 boys' group, Maharashtra's Deepak Mandal and Tanay Punjabi fought their way into the quarter-final round of the main draw.
Another Maharashtra player Advait Adik, seeded 3/4, also advanced to the last eight by outclassing Karnataka's Tarun Mammen 11-5 11-7 11-5 in 18 minutes.
Other results: Boys U-15 (Pre-quarter-finals): 1-Yash Fadte (Goa) bt Nikhil Jason (TN) 11-7 11-3 11-5; Sankalp Anand (DL) bt Arman Darukhanawalla (MH) 11-4 11-7 11-0; 3/4- N Avaneeth Prabhu S (TN) bt Lakshit Bohra (RJ) 11-5 11-6 6-11 11-4; Shivamraaj Gulati (CH) bt Kanhav Nanavati (TN) 11-8 13-11 11-9; 2-Neel Joshi (MH) bt Shreemann Raghavan (TN) 11-8 13-11 11-1.