After the selection, Foster said he wouldn't need another surgery to repair the issue, and the Niners front office has been adamant they are comfortable with his shoulder.
Speaking to KNBR-AM in San Francisco on Thursday, Kyle Shanahan said while the team remains confident in Foster's health, the coach admitted the "worst-case scenario" could affect the linebacker's contribution as a rookie.
"The worst-case scenario is the shoulder doesn't heal correctly and you've got to do it again," Shanahan said, via Eric Branch of the San Francisco Chronicle. "When you have to do it again, you have to get another surgery and it would be tough to play this year, and you end up having him the next year.
"But it's not something that would hurt him long-term. So the worst-case scenario, he wouldn't end up being able to play for us right away. But I still don't think how that would have changed how I personally felt about taking a guy with the 31st pick with the caliber of player that we took."
Foster was expected to be drafted in the top 10 last week, but some teams reportedly were troubled by the medical issue. Shanahan reiterated Thursday that the 49ers' medical staff is confident the linebacker's shoulder won't be a long-term problem.
"Our doctors do a great job," Shanahan said. "They looked into everything with Reuben and met with him. Our doctors felt good about his shoulder. They thought it was recovering well. They didn't have the same report a lot of other teams did.
"You never know who is going to end up being right. Everyone is trying to do their best to figure it out. But no one can tell the future. I just look at it as -- you go with what your doctors say. And then you always think about 'OK, what about the worse-case scenario?'"
With one of the least talented rosters in the NFL, the 49ers took a chance on a difference-making player with injury issues. The actual worst-case scenario is Foster never returns to being the hard-hitting destroyer he was at Alabama, and the Niners whiffed on another injured player. It's a scenario Shanahan doesn't see playing out, even as he admits the shoulder troubles could hinder Foster in 2017.