Feng, who took a one-stroke lead into the second round, had three birdies and a bogey in a two-under 70 that gave her the clubhouse lead on eight-under par 136.
But on the course, 17-year-old South Korean amateur Choi Hye-Jin was five-under for the day and eight under for the tournament through 14 holes.
The action on the course was underway when Trump arrived at the club in a fleet of black vehicles.
He was later spotted standing in a glass enclosed viewing area near the 15th hole.
The US Golf Association had faced calls to move the tournament after Trump's controversial remarks about women during his presidential campaign.
But fans at the course seemed glad to see the president, cheering as he waved to the crowd. Trump coming to the window several times as people snapped pictures and marshals reminded them to keep their voices down as play continued on the nearby green.
Feng's nearest rival in the clubhouse was South Korean Lee Jeong-Eun6, who carded a second straight 69 for a six-under total of 138.
Lee birdied the par-4 second, took her lone bogey at the par-4 fifth but closed the front nine with a birdie and added back-to-back birdies at the par-3 14th and par-5 15th to top the leaderboard at six-under 138 after the early wave of players.
Lee has the designation "6" after her name in scoring because she's the sixth of six women with the same name to play on the Korean LPGA Tour. Last year's Rookie of the Year on the KLPGA, she is making her first appearance in the United States.
World number one Ryu So-Yeon of South Korea was in the clubhouse on 140 after a second-round 72. She was joined at four-under by Spain's Carlota Ciganda, who completed her storm-interrupted opening round of 69 on Friday morning then posted a second-round 71.
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