Daniel Kilgore was glad he got a call from 49ers general manager John Lynch.

“I appreciated that,” the center said.

And tight end Vance McDonald was impressed that head coach Kyle Shanahan took the time to call in the midst of the NFL draft.

“The first thing I told him was ‘Man, there (aren’t) a lot of coaches that would do this,’” McDonald said.

And inside linebacker NaVorro Bowman was also happy Shanahan reached out.

“I wasn’t expecting it,” Bowman said, “but it was good to chear from him.”

Yes, the 49ers’ new regime possibly has made starters such as Kilgore, McDonald and Bowman uncomfortable with its competition-creating moves this offseason, but the decision-makers have followed those moves with a phone call. And, in the cutthroat NFL, the fact that Lynch and Shanahan have taken time to explain their decision-making is unique.

“In this business,” Kilgore said, “sometimes guys can get blindsided.”

Kilgore didn’t expect his GM to call after the 49ers threatened his starting spot in March by trading for Baltimore center Jeremy Zuttah, a Pro Bowl alternate last year. Similarly, McDonald heard from Shanahan after he learned he was the subject of trade talks, and Bowman spoke with him shortly after the 49ers drafted another inside linebacker — Alabama’s Reuben Foster — in the first round.

So what’s the motivation for reaching out? Some of it is certainly inspired by Lynch, an ex-safety who learned from Tony Dungy, his head coach for six seasons in Tampa Bay, about the proper way to treat players. For example, Dungy believed all players — regardless of their status — should hear from the head coach and general manager when they get released.

It’s “just the right thing to do,” Lynch said to Peter King of MMQB.com in April. “Even the bottom-of-the-roster guys, you talk to everyone you release. I told Kyle when we started there’s certain things I want to do different. I don’t care if it’s the back end of the roster, you and I both should meet with them. It’s a tough deal when your dreams are shattered.”

For Kilgore, McDonald and Bowman, their dreams weren’t shattered, but their standing on the roster was threatened.

And they’re hardly alone. The 49ers have added 50 players to their 90-man roster since Feb. 21, which means, in effect, they have two nearly evenly split camps in their locker room: the old guys and the new guys.

“Everybody’s new,” Kilgore said. “I think the only guys that are left are you guys (reporters), and myself, (Joe) Staley, NaVorro and Ahmad (Brooks). … And the kitchen staff.”

Given the upheaval, Lynch and Shanahan are wise to smooth over any ruffled feathers their offseason moves might have caused with the holdovers. Beyond being a decent thing to do, the calls could help eliminate tensions and insecurity felt by players who were part of the old regime.

It sounds as if Lynch and Shanahan have struck a familiar note in their calls: It’s not personal; we’re trying to improve a two-win team.

“It was nothing that I’d done,” said Kilgore, whose previous backup, Marcus Martin, was released in March. “They just wanted the competition.”

Said McDonald: “If you’re a 2-14 team, there are a lot of things you can improve on … So if teams are going to call and inquire about you, then obviously the next step is going to be see what it requires for the trade.”

Still, there’s no question players such Kilgore, McDonald and Bowman, who have combined to miss 66 games because of injury the past three seasons, have been put on notice.

In addition to Zuttah, the 49ers signed center Tim Barnes, a starter for the Rams the past two seasons. McDonald’s position group now includes fifth-round pick George Kittle and Cole Hikutini, an undrafted rookie who received $100,000 guaranteed to sign. And, if Bowman has a setback in his return from a torn Achilles, Foster and free-agent signee Malcolm Smith are on the roster.

In other words, changes figure to keep coming. And some holdovers who got a call during the offseason, could have a dream-shattering discussion with Lynch and Shanahan before the start of the regular season.

“They do run a tight ship,” Kilgore said. “They do want an (atmosphere) of competition.”

Eric Branch is a San Francisco Chronicle staff writer. Email: ebranch@sfchronicle.com Twitter: @Eric_Branch

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