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A scenario where Kaepernick will not play in 2016

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The moment Blaine Gabbert’s deep pass to Torrey Smith went way off target for an interception, KNBR sports writer Kevin Jones was disappointed. He wanted to see Colin Kaepernick get a chance to make that throw in a meaningful game.

But meaningful games are now pretty much over for the 49ers.

With NaVorro Bowman out for the season and the 49ers defense completely underachieving, the window for Kaepernick to play seems to be closing. NFL jobs are precious, so Chip Kelly is going to have to distance himself from Baalke while also keeping himself mistake free in Year 1, according to Jones.

“I’m starting to realize why Chip Kelly doesn’t want to play Kaepernick,” Jones said. “You have $14.5 million to lose and Kelly is responsible for his health. Trent Baalke is going to be able to point to that in a meeting. Kaepernick has now become a chess piece in the long term battle between Baalke and Kelly.

“Kelly needs to resist playing him. I’ve know I’ve been beating a drum for him to play, and nobody obviously wants to play Gabbert all season. But if Kelly messes this up, it will be a win for Baalke and another reason the GM could keep his job and own control over the 53-man roster.”

Jones argues that if Kaepernick had started and beat the Cowboys, he could theoretically beat the Cardinals and then the move to bench Gabbert would’ve been correct. And who knows? Kaepernick might’ve been able to hit Smith on that deep pass in the fourth quarter.

But if the 49ers lose on Thursday Night Football to Arizona, they’ll be 1-4 with a cross country trip looming to Buffalo. The season will be headed for the drain and you don’t want to lose the $14.5 million you’ll owe Kaepernick if he won’t be able pass a physical next April — on top of going 4-12. Jones thinks there’s a chance Christian Ponder sees the field before Kaepernick.

“I can see that really late in the year if it’s bad,” Jones said. “If it’s 2-10, you’re going to have to do something.”

Jones was joined by KNBR managing video editor Josh Lander in this week’s episode of 49ers recap.