SANTA CLARA, Calif. — In the hour before the San Francisco 49ers began practice Wednesday afternoon, coach Kyle Shanahan and general manager John Lynch expressed their hope that wide receiver Brandon Aiyuk would participate.

The reason for that unrewarded hope? Aiyuk’s clean bill of health from 49ers team doctors.

But during the roughly 30-minute window during which the media is allowed to watch the practice, Aiyuk was nowhere to be seen. Which brings Aiyuk and the Niners to the final and perhaps most explosive point in this long-running contract dispute.

Before Wednesday, Aiyuk was considered a “hold in” because he reported to training camp on time and attended meetings with the rest of the team. When Aiyuk reported, Shanahan said the wideout was dealing with back and neck pain. Those injuries allowed Aiyuk to avoid practice without incurring $40,000-per-day fines.

After the Niners trimmed their roster to 53 players on Tuesday, Aiyuk was cleared by the medical staff, Shanahan said. That clearance was the driving force behind Shanahan’s statement that he hoped Aiyuk would practice on Wednesday, with Lynch later adding that Aiyuk working out was “the expectation.”

Because Aiyuk, who Lynch said was at the team facility earlier Wednesday, was not at practice, the Niners now have the ability to pursue disciplinary action against the receiver. Under the terms of the collective bargaining agreement, once the league transitions from training camp to regular-season mode, teams can begin fining players for “unauthorized missed activities,” which can include walk-throughs, curfews, practices and meetings. Those fines can go up to $16,009 for each missed activity, with a maximum total fine for a single day of $45,769 if a player misses multiple events on the schedule. From there, teams also have the ability to suspend players for behavior that is detrimental to the team.

When asked on Wednesday whether they would punish Aiyuk for not attending practice, Lynch and Shanahan declined to say, but they did not rule out the possibility.

“I’ll deal with it if it happens. If it happens,” Shanahan said.

Lynch was later asked if the Niners had informed Aiyuk in recent weeks that he would be practicing starting Wednesday.

“I’m not going to comment on our communication,” Lynch said. “At some point you’ve got to play.”

Aiyuk is seeking a lucrative contract extension, either from the 49ers or another team. He missed all 20 of the 49ers’ pre-cut-down practices and three preseason games as he and the team went back and forth over multiple scenarios. That includes negotiating a long-term contract extension that would keep Aiyuk in San Francisco for the long haul, as well as trade talks with other teams, namely the Pittsburgh Steelers, New England Patriots, Cleveland Browns and Washington Commanders.

But so far, none of those conversations have resulted in an extension with the Niners or the right combination of trade compensation for the Niners plus financial compensation for Aiyuk to reach a resolution. With the season opener against the New York Jets scheduled for Sept. 9, the clock is ticking to find common ground. That could still result in a third option for Aiyuk: playing this season for the Niners on the fifth-year option, which guarantees him $14.124 million.

“As I think I’ve said from the beginning, we’ve reached a point where all options are possible,” Shanahan said. “And that hasn’t changed.”

Shanahan also acknowledged that Aiyuk’s unsettled status has contributed to the Niners keeping seven receivers on the initial 53-man roster. Despite all the back-and-forth in what has become a stare-down between the sides, Lynch again expressed hope that they can “break through.”

“I’ve seen these things look serious before, and they can turn around quickly,” Lynch said. “So that gives you hope, that we’ve been in these situations before and these things can be forgotten quickly. We remain hopeful.”

Aiyuk isn’t the only key player the 49ers are trying to bring back. Left tackle Trent Williams continued his holdout on Wednesday as he seeks a modified contract that offers significant guarantees and puts him back at the top of the tackle market.

Lynch said there has been “great communication” with Williams and that the Niners are “constantly working” on floating ideas and finding a solution to get the star tackle back into the mix. Unlike Aiyuk, Williams has not reported and remains on the reserve/did not report list, meaning he is not on the 53-man roster.

During Williams’ absence, Shanahan and Lynch have expressed confidence that the star player would return when the time is right. Still, there’s a growing sense of urgency to get Williams back sooner rather than later as Week 1 quickly approaches.

“I’m optimistic that Trent will be okay,” Shanahan said. “I’m sitting here not knowing what day it’s going to be. We’re getting close to playing a game, so I’m all about preparing for a game without those guys. But yeah, I think when two sides want to make a deal, that’s usually what happens.”