Samuel suffered a Jones fracture in his left foot during a player-organized practice in June while in Tennessee.
"Deebo was really working," Lynch said on the Murph and Mac show. "That's the wonderful thing we've learned about this kid ... He's a worker. He wants to be great at football, and that sure showed in his first year. But I think it's even showed more on his desire to be great.
"He was working tremendous when our players were down in Nashville doing some workouts that Jimmy (Garoppolo) designed and put together. Unfortunately, just a freak deal. A Jones fracture in his foot. So that was a blow. But I think you always try to be optimistic. The good news is it happened when it happened."
Samuel has insisted that he will be ready for the regular season, giving fans a 10-week timeline for his recovery. That would mean getting back onto the field by the end of August, which Lynch doesn't sound as optimistic about.
"Might we be without him a little bit at the beginning of the season? Yes," Lynch continued. "That timeline, sometimes these things heal at a different rate. They continue to monitor it. He's doing well. I'm not going to put an exact timeline on it, but I think it's fair to say that he may well miss some games early in the year.
"But we're going to have him back, at some point, and I know his rehab is going very well. And he's working very diligently and still intent on having a really big year for us. That's the good news of it."
Samuel caught 57 receptions for 802 receiving yards and three touchdowns through 15 regular-season games during his rookie campaign last season. He added 10 receptions for 127 yards through three playoff games, including a five-catch, 39-receiving-yard performance against the Kansas City Chiefs in Super Bowl LIV.
You can listen to the entire conversation with Lynch below.
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