SANTA CLARA, Calif. — After the San Francisco 49ers made significant tweaks to the contracts of defensive tackle Javon Hargrave and receiver Deebo Samuel Sr. in recent months, it left questions about whether both players were on their way out.

On Wednesday, Niners general manager John Lynch provided answers to those questions, revealing that the team plans to release Hargrave with a post-June 1 designation when the new league year starts in March. There are no such plans for Samuel, however.

“Deebo is under contract,” Lynch said. “[He’s] a good player and has done a ton for this organization and we’re not in the business of letting good players out of here.”

The 49ers restructured Samuel’s contract in September, a move that meant if the Niners were to trade or release him before June 1, 2025, they would have to absorb a $31.55 million dead money hit on the cap. If they did want to move on from him with a post-June 1 designation before his March 23 option bonus is due, they could have decreased that number to cap hits of $10,751,753 over the next couple of years.

But while Samuel is coming off a disappointing, injury-plagued season in which he finished with 806 scrimmage yards and four touchdowns (career lows save for a 2020 season in which he played just seven games), he looked more like himself against the Miami Dolphins in Week 16 and said he had “no questions at all” about his future in San Francisco.

Hargrave, however, will not be back unless it’s on a significantly reduced contract after the team makes his release official. That can’t happen until March 12 when the new league year begins. He restructured his contract in early December to make a post-June 1 release more palatable for the Niners.

The post-June 1 designation means Hargrave will count $8.6 million in dead money in 2025 and $17.485 million in 2026 as opposed to a nearly $25 million hit in 2025 without the designation. Hargrave signed a four-year, $84 million deal with the 49ers in 2023, but he played in just three games in 2024 before landing on injured reserve with a partially torn right triceps.

“We do have some challenges and so this doesn’t mean we can’t compete for his services,” Lynch said. “Rather than waiting until post-June 1 and being [out of luck] because free agency already happened, it gives him an opportunity to go see what his market is. And that may include us. … We know Javon. He’s on a good track coming back from his injury. And would we be interested in having him? Of course. Is that something we can come to an agreement on and is it something that fits in our plans? We will see.”

Lynch also offered an encouraging update on left tackle Trent Williams on Wednesday. Williams missed the final seven games because of a bruise in his left ankle. Over the final weeks of the season, Williams was seen in the locker room using a scooter to keep the ankle elevated, though he was walking without the scooter Friday before the season finale against the Arizona Cardinals.

Lynch confirmed that Williams, 36, intends to return for his 15th season in 2025.

“Trent’s doing well,” Lynch said. “It probably took a little longer than anyone anticipated [for the ankle to heal] but sometimes that happens, and the good news is it’s taken a positive turn. Trent’s mindset is where it always is, and he’s still very interested in being the great player that he is, and I think he’s still got a lot left in the tank. Trent’s as committed as ever and we love having Trent Williams a part of us.”

Upon his return, Williams will walk into an offensive meeting that features a coordinator for the first time since 2021 when current Dolphins coach Mike McDaniel held the title. Niners coach Kyle Shanahan announced Wednesday that while he’s looking for new defensive and special teams coordinators, he’s ready to promote Klay Kubiak to offensive coordinator.

Kubiak has been with San Francisco since 2021, holding the roles of defensive quality control coach, assistant quarterbacks coach and, most recently, offensive passing game specialist.

According to Shanahan, Kubiak has effectively been the offensive coordinator in recent years but hasn’t had the title. Shanahan will continue as the primary playcaller but Kubiak will continue to have a big say in the game plan and get the occasional chance to call plays as he did against the Arizona Cardinals in Week 18.

“I think Klay’s done as much as anyone on offense these last two years,” Shanahan said. “This is his second year doing that and he gets better and better each year at it. Just hasn’t had the official title yet and now he’ll get the official title, which he more than deserves. But it’s more about recognizing what he’s already been doing at a high level.”

As for replacing defensive coordinator Nick Sorensen and special teams coordinator Brian Schneider, Shanahan said that process is ongoing. Shanahan acknowledged Wednesday that he would like to keep Sorensen in another role and said Sorensen could be a candidate for the special teams job. At defensive coordinator, Shanahan said he would likely interview Brandon Staley, an in-house candidate who interviewed last year before the job went to Sorensen, but also said there will be external candidates who get an opportunity.

“I feel there’s some options out there that can end up being a better option in the situation that we’re in for our team,” Shanahan said. “I’m still hoping that we can keep Nick here, but I do feel there’s some other avenues that in the long run will be better for the 49ers.”