A week ago, Colin Kaepernick’s future represented a football problem for the San Francisco 49ers. Today, it’s a little more difficult. The quarterback’s national anthem protest has put the organization at a complicated crossroads, where the realities of salary, performance, protest and optics all merge into the same lane.

Now the 49ers have less than a week to choose a direction with Kaepernick. And it likely won’t be appealing – whether he remains on the roster or not.

While the NFL landscape surrounding Kaepernick’s protest has been filled with support and condemnation, the stance on his football career is a little less debatable. Kaepernick has continued slipping. And the 49ers noticed this long before his national anthem protests became a national lightning rod. Even before Kaepernick’s anthem stance, two personnel sources told Yahoo Sports the quarterback wasn’t making the progress hoped for in coach Chip Kelly’s offense. While there was no clarity offered on the 49ers potentially cutting Kaepernick, the bottom line was clear: The optimism of Kelly’s offense successfully rebooting the quarterback’s career had developed considerable doubts.

View photos Colin Kaepernick might not make the 49ers’ 53-man roster. (AP) More

Had football been the only factor, the thought of the 49ers releasing Kaepernick was problematic enough. It would come after an offseason when San Francisco had motivating factors to cut ties with the quarterback at least twice: once via a weeks-long trade dalliance with the Denver Broncos; another via a contract deadline that would have allowed the 49ers to cut Kaepernick before April 1 and void his $11.9 million base salary for this season.

But rather than cut him loose, the 49ers kept Kaepernick in the fold, hoping Kelly’s offense would resurrect a player who led the franchise to the Super Bowl after the 2012 season. This despite Kaepernick demanding a trade in the offseason and a locker room that had already seemingly embraced Blaine Gabbert as the team’s starting quarterback.

Keeping Kaepernick – and paying him – seemed to make it a virtual certainty that he would be in San Francisco for at least one more season. But the sources indicated there has been some frustration with Kaepernick’s progress since the offseason activities began. A large part of the problem has been his seemingly continual physical limitations due to nagging injuries. The 49ers hoped he would dive into the offseason with renewed vigor under Kelly, who offered him a clean slate. Instead, he missed the most rigorous portions of the offseason program and never gained the necessary traction to persistently challenge Gabbert for the starting job.

As the preseason whittled away, those realities started to make another factor more pressing. Specifically, the terms of Kaepernick’s deal call for a career-ending injury to lock in prearranged salary guarantees. If Kaepernick suffers a career-ending injury this season, the 49ers are on the hook for $19.7 million in guaranteed salaries ($14.5 million in 2017 and $5.2 million in 2018). But there’s a rub that works in the team’s favor: As part of his deal, Kaepernick purchased an insurance policy that awards $20 million to the 49ers in the event of such an injury. In essence, the 49ers are covered even if Kaepernick’s career comes to a sudden catastrophic end.

That insurance policy was supposed to take some of the risk out of the later stages of Kaepernick’s contract, making it more palatable to retain him, even if he was relegated to backup status. But the contract also contains offset language, which means the 49ers could cut him loose and not be held responsible for an amount matching whatever another team pays him. Should he be released and land a $3 million contract elsewhere, the 49ers save not only that money, but also avoid a $1.125 million roster bonus that kicks in when the 53-man rosters are finalized on Saturday.

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