He ceded kickoff return duties to Deonte Thompson late last year but remains the incumbent as the top punt returner.
Randall Cobb is assuming the punt return duties from Tramon Williams and competing with Alex Green for kick returns.
Thomas has been sharing return duties with Hixon and the third-round pick Jerrel Jernigan.
Coach Urban Meyer said Chris Rainey, Jeff Demps and Joe Haden would take over James's punt and kickoff return duties.
Mike Thomas and Cecil Shorts are competing for punt return duties, while Thomas is expected to handle kicks.
Brown averaged 10.8 yards on punts and 27.3 yards on kickoffs, though Emmanuel Sanders could resume kick return duties this season.
He will start in the nickel package, with potential to play at least half the defensive snaps, and compete for punt return duties, too.
Such was the sparkling nature of his debut – that also included punt and kick return duties – that Niners coach Jim Tomasula has been forced to quieten expectations.
Against Boston College, running back Da'Rel Scott handled some of the kickoff return duties, but Smith returned two for 38 yards.
He eventually lost his kick return duties to Danieal Manning, but began receiving more playing time as a wide receiver.
Hester was given back his kick return duties, and returned 2 kicks for 100 yards including a run back of 68 yards.
