SANTA CLARA, Calif. -- After trading star defensive tackle DeForest Buckner to the Indianapolis Colts in 2020, San Francisco 49ers general manager John Lynch called it the most difficult decision he'd made since taking the job three years earlier.

Similarly tough scenarios have emerged since, most recently with right tackle Mike McGlinchey, the No. 9 overall pick in the 2018 draft. McGlinchey wanted to stay in San Francisco and the Niners wanted to keep him, but it was clear long before McGlinchey signed a five-year, $87.5 million deal with the Denver Broncos in March that the sides were headed for a breakup.

At the heart of those choices has been the either/or decisions between standout players that most teams would love to have. In 2020, it meant Buckner was out, as fellow defensive lineman Arik Armstead stayed. This year, it was McGlinchey on the move because Williams signed a deal in 2021 that made him the game's highest-paid offensive tackle. To a lesser degree, the 49ers chose to re-sign linebacker Dre Greenlaw rather than retain Azeez Al-Shaair.

All of which sets the table for what could be San Francisco's next big contract dilemma: what to do with receivers Deebo Samuel and Brandon Aiyuk. Given that Samuel signed a three-year, $71.55 million extension in August, it might seem too early to discuss. But with Aiyuk eligible for an extension and coming off a season in which he, not Samuel or Pro Bowl tight end George Kittle, led the team in receiving, he's well on his way to a big payday.

"It's a good question," Lynch said. "It's a fair question because I understand the line of thinking. You can't keep everyone."

That line of thinking, combined with the 49ers receiving calls from teams interested in acquiring Aiyuk, was enough to have people wondering whether the Niners might actually move him this year. The rumor mill worked so hard during draft week that Aiyuk, the No. 25 pick in the 2020 draft, had moments of doubt. On April 28, Aiyuk tweeted that he got a call from his agent who was "just chattin" but he was worried that it might be the call that he'd been dealt.

Why my agent call me first thing this morning.. just chattin 😮‍💨🤣I thought I was up outta thrr I was gone head to the facility and start kicking doors down!!!!

— BA (@THE2ERA) April 28, 2023

While Lynch and Shanahan insist they will listen to calls on anyone -- they joke that they'd trade each other if the offer is good enough -- they never intended to do anything but keep Aiyuk for 2023.

The Niners have kept Aiyuk and picked up his fifth-year rookie option before the May 1 deadline, which guarantees him a $14.124 million base salary for the 2024 season if he doesn't sign an extension before then. Therein lies the 49ers' predicament. Traditionally, they prefer not to sign first-round picks to an extension until after their fourth season. That will happen later this summer with defensive end Nick Bosa, who will likely become the league's highest-paid defender when his deal is done.

If Aiyuk is able to build on the 78 catches, 1,015 yards and eight touchdowns he posted in 2022, there's a legitimate argument that he's not only San Francisco's best pure pass catcher but also one of the league's emerging receiver talents. Considering the rising cost of top wideouts, the Niners would theoretically have to decide between Samuel and Aiyuk.

That might happen eventually, but there's also a path for the Niners to delay that decision at least another year as they continue to chase their elusive sixth Lombardi trophy. Samuel's salary cap number for 2023 is an affordable $8.65 million, while Aiyuk's is a little less than $4 million. Their combined number jumps from $12.65 million to a whopping $42,696,000 in 2024.

But under normal circumstances, most first-round picks signing a lucrative long-term deal will have a more manageable salary cap figure in the first year than they would have if they played on the fifth-year option. Samuel's cap number in 2022 after signing his extension was $6.88 million and doesn't drastically spike until 2024 ($28.5 million). That's still a significant investment. but it's not outrageous to think the Niners could keep Samuel and Aiyuk together for another couple seasons by structuring an Aiyuk extension in a way that limits his short-term cap hits.

Regardless, the Niners view Aiyuk differently than players like Buckner and McGlinchey largely because of their evolution as a franchise. The Niners made some of their previous decisions to attempt to extend their Super Bowl window as long as possible. Their current choices are made in an effort to jump through that window before it closes.

"We're trying to do something special this year and Brandon is going to be a big part of that and beyond as well," Lynch said. "You always have to think out a few years but we're really excited about Brandon. I feel like he made another big step last year, and I think the best is yet to come and so we want him being a part of it.

"As of right now and into the future, we're really excited about Brandon Aiyuk and where he is at as a pro."

One other important factor in how this might play out: the Niners' belief in quarterback Brock Purdy. Purdy is expected to step back into the starting role this season and beyond once he recovers from right elbow surgery. Purdy isn't eligible for a contract extension until after the 2024 season and has cap hits of $889,253 and $1,004,253 in 2023 and 2024, respectively.

That bargain rate coincides with massive cap jumps for Kittle, Williams and linebacker Fred Warner. It also goes a long way in allowing the Niners to afford to keep their nucleus for at least two more seasons and sign big-ticket free agent defensive tackle Javon Hargrave. And if Purdy delivers and earns a lucrative deal of his own, San Francisco will then have even more onerous decisions to make.

"That was the whole goal," Shanahan said. "If we could get a quarterback on a rookie deal to play at a high, high, high enough level that we thought we could win with, then we thought we could build our team."