The versatile defensive back suffered a torn pectoral muscle in June.
"That's a tough one for us," Lynch told reporters. "The earliest we might have had D.J. back was early November. It's a four-to-six-month injury, so that's been an active conversation Kyle and myself and the medical folks have been having. Ultimately, too difficult to keep a roster spot for something that may go into December. So we made that (decision)."
Another move was that wide receiver Richie James Jr. would move from the reserve/COVID-19 list to the active/non-football injury list. James suffered a broken wrist/hand injury in June.
In addition to those moves, defensive tackle Kentavius Street (knee) and wide receiver Shawn Poindexter (ACL), two players who landed on injured reserve before the start of last season, were moved from the active/physically-unable-to-perform list to the active roster. That move may not hit the transaction wire until tomorrow, though.
Lynch added that no 49ers players had informed the team of a desire to opt-out of the upcoming season due to the coronavirus pandemic.
"None of our players have intimated that that is an option, that they're going to be exercising [the option to opt out]," Lynch said.
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