Brown, who started the day four shots off the lead after an opening-round 69, is at 10-under 132 at TPC Wakefield Plantation.
Flores bogeyed three of the final six holes and is alone in second.
Kyle Thompson and Ryan Armour both had 66 and are another shot back.
Aiken native Matt Hendrix (69) is tied for 15th at 137.
Former Augusta State golfer Major Manning (75, 146) missed the cut.
EUROPEAN TOUR: In Fiano, Italy, Robert Rock shot 4-under-par 68 to take a one-shot lead over Chris Wood and Joost Luiten after the second round of the Italian Open.
Rock was 12-under 132 for the tournament as he seeks his first European Tour win. Six others were within two shots of the lead, including Italian favorites Matteo Manassero and Francesco Molinari.
Former Augusta State golfer Scott Jamieson, who trailed by one after the first round, shot 74 and is tied for 40th at 139.
CHAMPIONS TOUR: In Conover, N.C., Bob Tway birdied the 18th hole for 9-under-par 63 and a one-stroke lead after the first round of the Greater Hickory Classic.
On a hot day when Mike Goodes fired 28 on the front nine, Tway had a stretch of four consecutive birdies to start the back nine on the Rock Barn layout.
Goodes, who had six birdies in a row to shoot the lowest front-nine score this season on the 50-and-over tour, was a shot back along with Tommy Armour III, Joe Ozaki and Mark Wiebe. Mark Calcavecchia, Mark O'Meara and David Eger opened with 65s.
LPGA TOUR: In Springfield, Ill., Mindy Kim maintained her two-stroke lead in the LPGA State Farm Classic, following her opening career-low 64 with 5-under-par 67.
Top-ranked Yani Tseng (66) and Shanshan Feng (65) were tied for second.
Jiyai Shin aced the par-3 second hole en route to 68 to reach 10 under.