49ers GM “absolutely” expects unhappy Colin Kaepernick to remain on roster as SF’s new coach Chip Kelly takes over

Here’s NFC West news from the league’s annual scouting combine that may make Seahawks fans smile, if not outright cheer, given the recent results in a diminished rivalry.

49ers general manager Trent Baalke said here Wednesday morning he “absolutely” expects unhappy, healing quarterback Colin Kaepernick to be on his and new San Francisco coach Chip Kelly’s roster past April 1. That’s the date on which Kaepernick is due $11.9 million from San Francisco.

“I expect him to come back,” Baalke said in a lounge area of Lucas Oil Stadium, site of combine workouts that began Wednesday. “The main thing is his health.”

Dialed-in Matt Barrows, my former Sacramento Bee colleague, describes why Kaepernick isn’t happy with the team and how he’s had three surgeries since November, all outside the 49ers’ medical staff.

Baalke didn’t commit Wednesday to Kaepernick being the 49ers’ starter for Kelly’s new schemes in 2016. And how could he? Kaepernick started only eight games last season, then went outside team doctors to have surgeries on his left shoulder, left knee and right thumb. Blaine Gabbert finished last season as San Francisco’s starter and won three games, to Kaepernick’s two.

Kaepernick completed only 13 passes for 124 yards in October while the Seahawks sacked him six times in Seattle’s 20-3 win in Santa Clara. That left him 1-6 in his career as a starter against the Seahawks. He’s lost to them twice as many times as any other team in the league.

Gabbert was 22 for 34 for 264 yards and a touchdown while getting sacked twice in San Francisco’s 29-13 loss at Seattle in late November, when Kaepernick was beginning his round of surgeries. Gabbert is 8-27 in his career, which was in Jacksonville from 2011 through ‘13.

Baalke said Wednesday he and Kelly believe the 49ers have two quarterbacks that can win in this league.

“We feel pretty good with the guys we have,” San Francisco’s GM said.

As for the new start with his third coach in two years -- Baalke won a power struggle with Jim Harbaugh following the 2014 season then flopped to 5-11 and last place in the NFC West last season with promoted assistant Jim Tomsula as head man -- Baalke had nothing but glowing remarks about Kelly. San Francisco hired him shortly after Philadelphia fired Oregon’s former coach this winter.

“It’s been awesome,” Baalke said of the transition. “Very easy to work with.

“He’s got an easy personality for us to deal with internally,” the GM said of Kelly, adding that may not be the case for the media that deal with the coach.

“It’s been an easy transition. We see eye to eye.”

This story was originally published February 24, 2016 at 9:33 AM with the headline "49ers GM “absolutely” expects unhappy Colin Kaepernick to remain on roster as SF’s new coach Chip Kelly takes over."