SANTA CLARA, Calif. -- One day after learning that he had lost out on the San Francisco 49ers backup quarterback job, Trey Lance was back at the team facility Thursday.

Barring a surprise, that's exactly where Niners general manager John Lynch expects Lance to be reporting to work for the near future.

Speaking to KNBR radio in San Francisco on Thursday morning, Lynch said that although the Niners are exploring all options -- including a trade -- for Lance, there's still a strong chance Lance will remain with the team as its third quarterback going into the season.

"That's the most likely option," Lynch said. "We're very happy with Trey. The most likely option is that he's here. If we can find a landing spot for Trey that is a really good one for him and works for our organization, that's not something that we'd turn a blind eye to. But that's not where our focus is right now. Our focus is on Trey getting back here and us being the best football team. We're getting close to Pittsburgh [in Week 1]."

Lance's status gained an additional dose of uncertainty Wednesday when Niners coach Kyle Shanahan informed him that the team is going with Sam Darnold as the backup to starter Brock Purdy. That left Lance, the No. 3 pick in the 2021 NFL draft, whom the Niners traded four picks (three first-round picks and one third-rounder) to acquire, disappointed.

So disappointed, in fact, that, after his conversation with Shanahan and then another with Lynch, the Niners excused Lance from Wednesday's practice to clear his head and come to grips with the current situation.

Lynch, who did not offer a clear answer when asked whether Lance had requested a trade, said it was a "gut punch" for Lance.

"Trey handled it incredibly well, with class," Lynch said. "He was devastated, and rightly so. When you put your heart and soul into something and it doesn't come to fruition, you're going to be devastated. That's the type of competitor he is. But we're in a good place, he'll be back in the building today and we're moving forward."

That plan remains for Lance to play in Friday's exhibition finale against the Los Angeles Chargers. Shanahan has said Purdy and most of the starters will play to open the game, then Darnold will replace Purdy, and Lance will follow Darnold.

It's unclear whether Brandon Allen, who has been the team's fourth quarterback throughout the preseason, will get any snaps against the Chargers.

For Lance, that exhibition finale will offer one more showcase opportunity to other teams around the league that might be interested in trading for him.

While Lynch denied that the Niners shopped Lance all offseason, he has previously acknowledged getting calls from interested teams in the run-up to the draft.

If the Niners trade Lance, he will count $5,540,956 in dead money over each of the next two seasons and the team will save $3.76 million in 2023 and $5.31 million in 2024 against the salary cap.

The Niners are unlikely to simply release Lance because he would count $14.61 million in dead money and incur an additional charge of $5,310,717, the fully guaranteed salary Lance is set to make in 2024. Given San Francisco's recent history of quarterback injuries -- they were down to fourth option Josh Johnson in the NFC Championship Game on Jan. 29 and ran out of quarterbacks when he suffered a concussion -- the team is all but certain to keep three quarterbacks on the roster.

Which means, barring a worthwhile trade offer, this could make Lance more valuable to the Niners even as a No. 3 quarterback than acquiring a future late-round pick.

"Trey made incredible leaps and bounds this year," Lynch said. "I think his games showed that. I really give him a lot of credit because we didn't like tailor an offense that highlights what Trey is able to do but I think he grew from that. He just played within our offense and still showed some of his ability to move around, made a lot of plays. Ultimately, Kyle and our coaching staff, they're tasked to make tough decisions and believe me this one was painstaking for them. They came to a point where they felt like Sam had won it and nothing was going to change that."

One player who still is not in the Niners' facility is star defensive end Nick Bosa. Bosa is still holding out as he awaits a lucrative contract extension expected to make him the league's highest-paid defensive player.

"I don't like the situation," Lynch said. "Since our tenure here we haven't had a holdout anywhere close to this magnitude. We're working really hard to try to change that. We're in communication with his reps. He's a special player, he's going to get a special contract. I can tell you that."