But Niners coach Kyle Shanahan and general manager John Lynch remained steadfast Wednesday that Bosa will sign a lucrative contract extension and that there's no scenario in which they would trade Bosa.
Shanahan said recently that Bosa's extension negotiations have gone about how he expected, even though Bosa has not been with the team since it opened training camp July 25. Asked if he thought it would drag on this long, Shanahan suggested this is the window he has had in his mind throughout the process.
"I thought it would come probably at this time, just looking at the history of those things," Shanahan said. "And I'm really hoping it gets done. I know they're working tirelessly at it ... but hopefully we can get him in here sooner than later."
Speaking for the first time since trimming to the initial 53-man roster on Tuesday, Shanahan and Lynch were adamant that even though Bosa's holdout has gone on longer than they'd like, they don't see any scenario in which he'd be traded.
"No, I feel pretty strongly and I think everyone would agree with that," Shanahan said.
Asked if there was even a percentage chance he'd consider trading Bosa, Lynch minced no words. "No," Lynch said. "Real simple."
Lynch added that there were no updates on Bosa's contract talks but did acknowledge there has been communication between the team and Bosa's agent, Brian Ayrault, and "that's a good thing."
The Niners have never shied away from the idea that Bosa deserves a significant pay bump that makes him among the highest-paid defenders in NFL history. Lynch has also said it's a process that requires patience as they look for the "sweet spot" that works for both sides.
San Francisco has a lengthy track record of paying its top players, reaching agreements with tight end George Kittle, linebacker Fred Warner and receiver Deebo Samuel either just before or right after training camp has opened the past three years.
Bosa's deal has proved more complicated, presumably because he's only 25 and coming off a season in which he won the NFL's Defensive Player of the Year award. Bosa led the league with 18.5 sacks last year and is entering the fifth and final season of his rookie contract at a price of $17.9 million.
It's possible Bosa's new deal could surpass the annual average value of Los Angeles Rams defensive tackle Aaron Donald ($31.67 million) and/or the full guarantees of Pittsburgh Steelers pass-rusher T.J. Watt ($80 million), both high-water marks for defenders.
"You guys know how we feel about Nick, and we all know how good of a player he is," Shanahan said. "Hopefully we can come to terms soon and get him here as fast as possible."
Another lingering issue for the Niners is at kicker, where they don't currently have a healthy option. The 49ers kept third-round pick Jake Moody on the roster, but he's dealing with a right quad injury that has cast doubt on his availability for Week 1.
On Tuesday, the Niners placed kicker Zane Gonzalez (right calf) on injured reserve, and the team has not signed another kicker to the practice squad. According to Shanahan, the Niners still plan to sign a kicker to the practice squad who would give them insurance in case Moody is unable to play in Pittsburgh. That could happen as soon as this weekend.
"I had no idea there were this many kickers out there," Lynch said. "I've gotten many texts from people who kicked at one point in their life, Pop Warner, to very accomplished kickers. That process has been good as well. Jake Moody has been tracking well. His recovery is going well, but we'll be prepared for anything."
Another Niner missing from Wednesday's practice was Kittle. Kittle also did not practice Monday and will not participate Thursday, according to Shanahan. Kittle suffered a groin injury a few weeks ago, and though he returned and played in the preseason finale, he's still dealing with the ailment.
"We're just taking care of him right now," Shanahan said. "It's still stuff lingering a little bit from him that has cost him some time. We're not going to practice him today either and hopefully we'll get him going on Monday."
Some eyebrows were raised Monday when quarterback Brock Purdy was not taking on his usual workload. Shanahan said the Niners are using this week to "deload" Purdy's surgically repaired right elbow, trimming his weekly throws from about 700 to 350.
The hope, according to Shanahan and Lynch, is that Purdy will feel fresh going into the first week of the regular season.