Shanahan confirmed that the 49ers voided those guarantees in July but declined to discuss the details behind the decision. He acknowledged disappointment in how the situation has unfolded.
"I've been coaching over 20 years, and I've never been in a situation where a contract's been voided," Shanahan said. "So it was extremely unusual to me."
The coach also verified that Aiyuk has missed meetings, as reported by The Athletic as one of the catalysts for the team's frustrations, but noted that such absences aren't uncommon for injured players.
"Any injured player, or people that are on IR or doing rehab, their schedule is totally different than the rest of the team," Shanahan explained. "So sometimes they're involved in meetings, sometimes they're not at all."
Still, Shanahan admitted that voiding a player's guarantees is a strong indicator of how serious the situation has become.
"It takes a lot of things to get a contract voided," he said. "Honestly, I've never dealt with that in my career or been in any building that's had that. So it was unusual, but that's stuff that I can't get into right now."
Despite the tension, Shanahan said the 49ers remain hopeful Aiyuk can return this season, describing his status as week-to-week.
"Hoping he can clear all the markers so he can come back and start his practice window," Shanahan said.
The coach added that there hasn't been much communication between him and Aiyuk in recent months. He's relying on updates from the medical and training staff, confirming that Aiyuk has not yet been medically cleared to practice.
"There's still markers he's got to pass," Shanahan noted.
When asked whether Aiyuk is motivated to return this season, Shanahan offered a blunt response.
"I don't think that really matters," he said. "I think everyone might have a different opinion of that. With the contract stuff, that happened back in July. I knew it was going to be a while for him to come back. I was hoping to get him back around this time, and we've kind of been going about that.
"But coaching the team, I don't really deal much with injured players. I was told a few weeks ago he was getting closer, and we haven't made progress in that way, so far. So, from my standpoint, I'm just waiting for him to get back to practice."
As for whether Aiyuk and the 49ers are truly headed for a split after the season, Shanahan pushed back on that narrative.
"What happened in July, to me, in my opinion, doesn't have anything to do with the future," Shanahan said. "That had to do with circumstances that, to me, were out of a coach's hand.
"The best way I can explain it, when it comes to business matters and lawyers and contracts and things like that, when it comes to the future of this, I would love for BA to be here. I would love for him to get healthy and get back to really helping us out and being a part of this team.
"We haven't had that in a little bit, and I still hold out hope that he can get there, but he obviously hasn't gotten there yet."
Shanahan understands the focus on this storyline, but for him, it's something that was dealt with back in July. His attention remains on this season and Monday night's matchup against the Carolina Panthers.
"What you guys found out yesterday, or that was public, I know that's unusual, so I get all those questions about it," Shanahan said. "But that is something that happened three or four months ago—whenever that was—and something that's been completely out of sight, out of mind in terms of a contract. The only thing I've been thinking about is hoping he can get healthy and come back and play for us."
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