49ers, Colin Kaepernick’s talk contract extension face-to-face for first time since Februrary | The Sacramento Bee

The 49ers, who on Sunday received enough salary-cap relief to accommodate a contract extension for Colin Kaepernick, wasted no time reviving long-dormant discussions with the quarterback’s representatives.

The two sides met at team headquarters Tuesday, which is believed to be their first face-to-face talks since they dined at a popular Indianapolis steakhouse during the NFL scouting combine in February.

That the sides are meeting again suggests the 49ers are convinced nothing will come from the police investigation in Miami that involves Kaepernick and two other players. That investigation began April 3 and created a lull in the negotiations.

The investigation is ongoing, but the hope is that it will be resolved by the end of the month. Team officials, in particular coach Jim Harbaugh, have strongly supported Kaepernick throughout.

“I feel very good there’ll be a good resolution, and hopefully a just one, too,” Harbaugh said in April. “I hate to see his reputation be the victim.”

The 49ers also now have the salary-cap space to move forward with a contract that almost certainly will make Kaepernick the highest-paid 49er and that could be one of the most lucrative in the league.

On Sunday, the 49ers received a $6.6 million boost to their cap surplus when former cornerback Carlos Rogers’ 2014 salary was wiped off the books.

The team gained another $2.6 million in cap space last month when all-pro linebacker NaVorro Bowman converted a portion of his base salary into a signing bonus.

Bowman’s restructure allowed the 49ers to sign their NFL-high 12 draft picks. They currently are about $8 million below the salary cap heading into the season. That’s enough to accommodate the initial cap hit on a new deal for Kaepernick.

Harbaugh, team owner Jed York and general manager Trent Baalke all have said that locking down Kaepernick long term is a priority for the team, and Baalke has said he’d like to have the deal completed by the start of training camp on July 23.

The 49ers have several other young players – guard Mike Iupati and wide receiver Michael Crabtree – they’d like to lock in for the long-term, and they likely will press that point with Kaepernick’s agents. Baalke argued in March that teams that sign quarterbacks to big-money deals rarely win Super Bowls because they can’t afford to surround those players with championship-caliber talent.

Harbaugh, on the other hand, said in March that he thought Kaepernick deserved to be paid the market rate, which when considering recent deals for the Cowboys’ Tony Romo and the Bears’ Jay Cutler, is at least $18 million a season.

“There’s really no one that competes with him in a workout situation,” Harbaugh said at the owners meetings in Orlando, Fla. “He will bury everybody. And then when somebody tries to compete with him, he ramps his competitiveness up, and somebody’s over their knee throwing up. He’s unbelievable. So you can tell I feel he’s a great player, a high priority.”

Also in March, Baalke said he thought negotiations would soon enter a new, more specific phase. Instead, the Miami investigation began and talks stalled.

Kaepernick’s agent wasn’t the quarterback’s only advocate on hand Tuesday. Kaepernick’s father, Rick, watched the 49ers practice alongside team owner John York.