Miller wrote the following about potential friction between the two in San Francisco — one that could lead to a breakup, according to the draft analyst.
"According to sources in the team's scouting and coaching staff, the two aren't in lockstep as far as the vision of the offseason and the future of the franchise. The coach, Shanahan, wants to scheme and develop players while not being bothered with the player evaluation process, but more and more he finds himself involved while not trusting the decision-making of Lynch—a former media analyst after his Hall of Fame playing days but not someone with a scouting background."
Lynch and Shanahan were brought in together in 2017 and signed to six-year deals. The duo is entering its third season together and has won just 10 games through its first two seasons with San Francisco.
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Miller goes on to speculate that a power struggle might be on the horizon with Lynch and VP of player personnel Adam Peters potentially on exit paths and Shanahan searching for someone else to run the draft and free agency.
49ers CEO, Jed York, recently expressed confidence in both Lynch and Shanahan while speaking to NBC Sports Bay Area in March. In fact, York is even more confident in Lynch and Shanahan now than he was when he hired the two in 2017. Much of that, he says, is based on observing how the duo works together and the plan it has mapped out. York loves the chemistry between the two.
"I see that in spades," he said. "It's just awesome to watch those guys work together."
That's why York has shown great patience in giving Lynch and Shanahan the time they need to rebuild the 49ers roster.
"You don't know what you don't know when you're in those positions," York added. "And I think it's been interesting to watch these guys really come together and show they're a stronger bond today than what they were two years ago and it's only getting stronger."
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