The 49ers had to sign veteran Ameer Abdullah Thursday morning because they're so thin at the running back position. Christian McCaffrey takes lots of days off, Israel Abanikanda recently got cut and rookie fifth-round pick Jordan James has missed the past two practices.
On Thursday, a reporter asked Shanahan why James is out.
"James has some knee issues," Shanahan said. "We're going to re-evaluate him throughout this week. See how it goes, how he recovers and then see where we are in a week.”

The 49ers don't know when James will return
If James' knee injury were minor, the 49ers would say so. They said that Mykel Williams' ankle injury that kept him out of Tuesday's practice was minor, and he was back on the field today.
Shanahan was intentionally vague about the nature of James' knee injury. But, when he referred to it, he talked about "issues," plural. Not "issue," singular. Which, again, sounds bad.
I'm guessing the 49ers are hoping that his issues aren't as bad as they fear and that a week of recovery will bring good news. It's also possible that the 49ers are debating whether they should shut down James for the season, and they'll make up their minds in a few days.

If James suffered something serious such as a torn MCL, he might be able to return midseason. But the 49ers might not want to rush a rookie onto the field in November. They might want to give him a full red shirt year. These are things they might be considering.
I wonder if the 49ers regret trading Jordan Mason to the Minnesota Vikings. James was supposed to replace him, but James is hurt. Meanwhile, Mason is having a terrific training camp in Minnesota and he's healthy.