Shankar, the 2014 PGTI Order of Merit champion was sitting pretty at a total of nine-under-135 at the end of round two.
There was a five-way tie for second place at seven-under-137 between Noida's Gaurav Pratap Singh, overnight leaders Gaurav Ghei and Shamim Khan of Delhi, Honey Baisoya, another Delhi pro, as well as Chandigarh's Ajeetesh Sandhu.
The cut came down at three-over-147. Fifty professionals made the cut.
The 33-year-old, who won the last of his six titles in late 2015, picked up two more strokes on the back-nine in what turned out to be a round of many near-misses for eagle and birdie.
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"I came into this week with the disappointment of not getting to play in the Asian Tour's Bangladesh event due to some issues with the visa. However, I've been able to put that behind me with two solid rounds here in Noida.
Local favourite Gaurav (67-70), who shared third place with Shankar after round one, moved up one spot courtesy a 70 that featured an eagle, two birdies and two bogeys. Singh came close to making an albatross on the par-5 first hole where he landed his second shot from 250 yards out to within inches of the pin. He picked up an eagle there.
Overnight leaders Ghei (66-71) and Shamim (66-71) slipped to tied second after posting scores of 71 in round two.
Ghei was two-over through the front-nine but a near-perfect tee shot on the 10th helped him settle down and he went on to add three birdies from there on.
Shamim, on the other hand, was four-under through the front-nine but a double-bogey and two bogeys on the back-nine meant he closed the day with a modest 71.
Patna's Aman Raj and Panchkula's Angad Cheema were in tied seventh place at four-under-140.
Among the rookies, Kolkata's Viraj Madappa (71-74) made the cut. Viraj, playing his first event as a professional, totaled one-over-145 at the halfway stage to be tied 21st.