Lynch told KNBR, "Yesterday was not encouraging," with regard to McKinnon's return to practice (h/t the San Francisco Chronicle's Eric Branch).
The Athletic's Cam Inman added more perspective:
NFL Network's Tom Pelissero reported McKinnon had a "flare-up" and that the 49ers are determining the extent of the situation before making their next move.
San Francisco signed McKinnon to a four-year, $30 million deal that included $18 million guaranteed last offseason. He was coming off a productive 2017 campaign in which he gained 991 yards from scrimmage and scored five touchdowns.
While the Niners planned on McKinnon being a part of their backfield in 2019, they also planned for the possibility his knee injury could continue to be an issue.
Matt Breida led the team in rushing yards (814) while averaging 5.3 yards per carry last season. Even if McKinnon is healthy enough to suit up in Week 1 on Sept. 8 against the Tampa Bay Buccaneers, Breida is San Francisco's primary ball-carrier.
The 49ers also signed Tevin Coleman to a two-year, $8.5 million deal to provide an aerial dimension at running back. Coleman had 92 receptions for 1,010 yards and 11 touchdowns in four years with the Atlanta Falcons. He can ease some of the rushing load on Breida as well.
The finances will make it tough for San Francisco to release McKinnon outright. Even as a post-June 1 cut, he'd count for $5.7 million in dead money for 2019, with only $50,000 in salary-cap savings.
Placing him on injured reserve and evaluating his long-term future at a later date might be Lynch's only move.