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

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

But during the roughly 30-minute window in which media is allowed to watch practice, Aiyuk was nowhere to be seen. That brings Aiyuk and the Niners to the latest and perhaps most volatile point in this drawn-out contract dispute.

Before Wednesday, Aiyuk had been considered a "hold in" because he reported to training camp on time and has been attending meetings with the rest of the team. At the time Aiyuk reported, Shanahan said the wideout was dealing with back and neck soreness. Those injuries allowed Aiyuk to avoid practice while not accruing fines of $40,000 per day.

After the Niners trimmed their roster to 53 players Tuesday, Aiyuk was cleared by medical staff, according to Shanahan. That clearance was the driving force behind Shanahan saying he hoped Aiyuk would practice Wednesday, with Lynch later adding that Aiyuk practicing was "the expectation."

Since Aiyuk, whom Lynch said was in the team facility earlier Wednesday, was not at practice, the Niners now have the option to enforce disciplinary action against the receiver. Under the terms of the collective bargaining agreement, once the league switches out of training camp and into regular-season mode, teams can begin fining players for "unexcused missed activities," which would include walk-throughs, curfews, practices and meetings. Those fines can reach up to $16,009 for each activity missed, 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 conduct detrimental to the team.

Asked Wednesday if they would punish Aiyuk for skipping practices, Lynch and Shanahan declined to say but didn't shut down that possibility.

"I'll deal with that when that happens. If that happens," Shanahan said.

Later, Lynch was asked if the Niners communicated to Aiyuk at any point in the past few weeks that he was expected to practice starting Wednesday.

"I'm not going to get into our communication," Lynch said. "At some point, you've got to play."

Aiyuk has been seeking a lucrative contract extension, whether 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 have gone back and forth on 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 discussions with other teams, namely the Pittsburgh Steelers, New England Patriots, Cleveland Browns and Washington Commanders.

But so far, none of those discussions has yielded 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 set for Sept. 9, the clock is ticking on finding common ground. That still could result in a third option for Aiyuk: playing out this season for the Niners on the fifth-year option, which guarantees him $14.124 million.

"Just like I think I've said from the beginning, it's reached a point where all options could happen," Shanahan said. "And nothing has changed on that."

Shanahan also acknowledged that Aiyuk's uncertain status contributed to the Niners keeping seven receivers on the initial 53-man roster. Despite all of 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 dire before, and they can quickly turn," Lynch said. "So that gives you hope, that we've been in these situations before and those things can quickly be forgotten. We will remain hopeful."

Aiyuk isn't the only key player the 49ers are trying to bring back into the fold. Left tackle Trent Williams continued his holdout Wednesday as he is seeking an adjusted contract that provides significant guarantees and elevates him back to the top of the tackle market.

Lynch said there's been "good communication" with Williams and that the Niners are "constantly working" to throw out ideas and find a solution to get the star tackle back in the mix. Unlike Aiyuk, Williams has not reported and he remains on the reserve/did not report list, which means he does not appear on the 53-man roster.

Throughout Williams' absence, Shanahan and Lynch have expressed confidence that the star tackle would return when the time is right. Still, there's an increasing sense of urgency to get Williams back sooner than later with Week 1 rapidly approaching.

"I'm optimistic that things will work out with Trent," Shanahan said. "I'm not sitting here knowing what day it'll be. We're getting close to playing a game, so my mind is completely on preparing for a game without those guys. But yeah, I feel when two sides want to get a deal done, usually it happens."