"What I can tell you, as of right now, we're not going to move Jimmy to IR," Lynch told KNBR's Paul McCaffrey and Markus Boucher. "I think we're just going to carry him on our roster, and we're going to kind of see how this rehab process goes. There's a natural healing process that has to take place."
Garoppolo suffered what was initially thought to be a season-ending broken foot on Sunday against the Miami Dolphins. The 49ers assumed he would need to undergo surgery with an estimated six-month recovery time.
On Tuesday, ESPN's Adam Schefter broke the news that doctors had updated the prognosis. Garoppolo would not require season-ending surgery, and the quarterback's recovery time may only be a fraction of the original estimate.
"The report from the doctors today (Tuesday) was much more optimistic and upbeat than the one on Sunday night after the game when doctors thought he would be six months," Schefter said Tuesday on ESPN, "when he would need surgery on the broken foot. The foot is broken, but it's possible now that he could be back in seven to eight weeks."
A day later, Kyle Shanahan expressed a lack of optimism regarding the potential return of his injured quarterback. The head coach informed reporters that there was no ligament damage, but the seven-to-eight-week timeline was when Garoppolo might be fully healed, not when he might be ready to step back on the football field.
"It's not a Lisfranc [injury]," Shanahan said. "They don't have to do surgery on it. Still going to be a big recovery, but much less than what we anticipated, which is awesome news for him."
Shanahan added, "Really, there's that way outside chance late in the playoffs or something like that, but it's just an outside chance. I'm not real optimistic about that, but you never rule it out."
Lynch agrees with the coach. Expecting Garoppolo to return for the playoffs might be a stretch.
"I think there was a lot of good news in that it wasn't the Lisfranc," Lynch said. "There weren't torn tendons and all that. There's a healing process that has to take place. How quickly it will heal, that's in the good Lord's hands, and so we'll sit back and see. I think we were encouraged, but I think Kyle also said it's also highly unlikely. It's a big ask.
"Jimmy's got a really bright future and a lot of years in front of him. We're not going to put him in a bad position. So we'll continue to consult with the doctors and let them kind of guide that decision. But there was some encouraging news earlier this week."
If the 49ers were to opt to bring Garoppolo back from the injured reserve list, that would leave the team with the ability to do so for only one more player. Both running back Elijah Mitchell and defensive tackle Javon Kinlaw are on the injured reserve list.
Rookie Brock Purdy will make his first start this weekend when the 49ers host the Tampa Bay Buccaneers. He is backed up by veteran quarterback Josh Johnson.
You can listen to the entire conversation with Lynch below.