Atwal, who shot 66 in the first round, is now six-under 136 to be placed tied 37th at the midway stage of the first event in the Fall series of the PGA Tour.
Atwal, teed off from the tenth and bogeyed the 11th, but birdies on 13th, 15th, 16th and 18th saw him turn in three-under at which stage he was in line for a top-10.
But a bogey on second and a double on sixth spoilt his card. A birdie on ninth, his closing hole of the day, was a small consolation.
Kevin Na (63) and Charlie Wi (66) joined Jhonattan Vegas (67) in shared lead at 12-under 130 after two rounds.
Play was suspended because of lightning near the course and then a second time the stoppage came with one player Fran Quinn (at three-under for the day) having one hole to play. The cut was likely to come at four-under and Quinn came make it with a birdie on last hole.