Pathania's second round effort took his total to nine-under-135, while Chandigarh's Harendra shot the day's best score of seven-under 65 that propelled him to second place at seven-under 137 at the Rs. 30 lakh event.
Pathania (69-66), lying overnight tied fifth, posted a bogey-free 66 to take pole position at the halfway stage. The 33-year-old from the Jaypee Greens Golf Resort picked up three strokes from a range of six to 10 feet and also capitalized on three of the four par-5s with birdies.
Harendra (72-65), who began the day in tied 30th seven off the lead, climbed into contention on Wednesday thanks to his improved ball-striking. The 31-year-old made good use of the advice he received on his swing from Bangladeshi professional Md Sayum last week in Dhaka.
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Pratap Atwal, the round one leader, followed up his opening round 65 with a 73 in round two, to slip to tied third at six-under-138. Pratap sank an eagle and a birdie but also dropped two bogeys and a double-bogey on Wednesday.
Ranjit Singh shot a second straight 69 courtesy his sharp chipping and putting to join Atwal in tied third. Ranjit, who made four birdies and a bogey on day two, chipped-in for birdie on the second and almost holed it from the bunker for eagle on the fourth.
Bengaluru's Udayan Mane, Delhi's Himmat Singh Rai were in tied 21st at one-under-143. Rookies Aman Raj of Patna and Noida-based Samarth Dwivedi, both playing their first professional event, also took a share of 21st place.
Pravin Pathare and Sagar Raghuvanshi closed round two in tied 27th place with totals of even-par-144. Fifty professionals made the cut.