While some feel McKinnon could land on injured reserve, at least for the short term, Lynch sounded a bit more optimistic about the running back.
"He had a great return from his ACL, and we were really just being cautious in the offseason," Lynch said on the "Murph and Mac" show. "The nature of his position, the running back position, it asks a lot of these guys. You have to cut hard.
"And so we kind of held him out but he was doing good, and our trainers and doctors kept saying, 'He could be out there but we think it's more wise just to kind of continue to rehab him on the side and bring him back in camp.'
"Unfortunately, he just had a flare-up. We gave him a couple of weeks off, but then he came back and pushed it hard, and it wasn't quite ready. We're having to exercise some patience, which is hard; most of all, hard on Jet. He's put so much work in, and I think he's been down. But I'm starting to see Jet, who's always smiling, smile a lot more. So it tells me he's feeling better.
"The communication with him is that he is feeling better, and I'm just hopeful and praying for him, because he's worked so hard, that he can come back."
Lynch said McKinnon remains an important part of the 49ers' plans. The running back is so much fun to watch, the GM added.
"He's a couple of weeks away from coming back and giving it another shot," Lynch continued. "We're hopeful that this time around, it's a lot better for everybody."
Could McKinnon be ready for Week 1 of the regular season? The 49ers GM isn't prepared to make any timeline predictions just yet.
"I think, physically, yes," Lynch responded. "I think it's hard to ask a running back to go play considerable snaps when they haven't done it in over a year. That's one nice thing about our running back room, though; we have a lot of depth.
"The addition of Tevin Coleman, when you add him to (Matt) Breida and the group we have, it gives us some ability to say, 'Let's take this a little slower.' Raheem Mostert can run the football with really good effectiveness.
"I think that's something we feel comfortable in doing, and maybe bringing Jet along a little slower. But we'll see. We'll just kind of let this play out, and we're going to get him ready as quick as possible, but we are deep at that position, so that will help us."
You can listen to the entire conversation with Lynch below.
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