Rathod started the slide of the fancied when he beat Girish in a 4-3 thriller after leading 3-1. Girish kept his hopes alive by snatching the fifth and sixth frames on the black, but Rathod surprised his opponent in the decider with another nail-biting black ball finish.
Merai upset Gulati with a significant 4-2 win, after leading 3-1, to advance to the final qualifying round.
Jayesh Salvi of Maharashtra completed the day of upsets when he beat state rival Sunil Jain 4-0.
Other significant second round winners were Rovin D'Souza, Manav Panchal and Gaurav Jaisinghani, all of Maharashtra, R Santosh of Karnataka and K Venkatesh of Railways.
Results: 2nd qualifying round: B V Rathod (AP) bt R Girish (Rlys) 12-39, 40-15, 36-20, 47-20, 37-40, 28-32, 39-33; Gaurav Prabhu (Mah) bt Kartik Jhaveri (Mah) 42-29, 16-44, 16-28, 29-38, 42-22, 40-32, 44-0; Subrata Das (Orissa) bt Avish Garg (UP) 36-29, 22-33, 35-17, 33-43, 30-14, 13-37, 32-9; R. Santosh (Kar) bt Shahbaaz Khan (Mah) 31-41, 54(47)-0, 42-16, 1-43(37), 40-15, 44-11; K. Venkatesh (Rlys) bt Hemanth Singh (AP) 37-5, 49-25, 30-8, 32-24; Jayesh Salvi (Mah) bt Sunil Jain (Mah) 26-18, 40-37, 46-19, 31-14; Gaurav Jaisinghani (Mah) bt Prabdeep Singh (Mah) 30-2, 11-42, 47-33, 8-38, 26-14, 46-8; Manav Panchal (Mah) bt Ishmit Singh Malik (UP) 40-1, 38-22, 52-13, 32-21; Rovin D