Kaepernick was granted permission to meet with the Denver Broncos after his agents requested a trade during the offseason.
"He's still here," Baalke said. "Right now, he's out there, he's practicing, he's doing good in his rehab, that seems to be progressing well. He's going to all the meetings, he's very into it, he's very attentive, he's working hard. The coaches are excited about it, just as they are about getting a chance to work with all these guys. And there's really nothing else to report."
"Gave him a headache? It's like me speaking to you, it gives me a headache!" Baalke said during his meeting with beat writers.
Kaepernick met with Broncos GM John Elway late last month at his Denver home, and it seems like the Super Bowl champions could be a potential fit for Kaepernick. Still, he is due $11.9 million guaranteed this season and might not want to restructure his deal for any less.
Davis was the 49ers' first-round draft choice — the 11th overall pick— in the 2010 draft out of Rutgers. He was affected by a concussion late in the 2014 season.
Kaepernick went 2-6 in eight starts last season, raising questions about whether the quarterback who guided the 49ers to a runner-up Super Bowl finish following the 2012 season was still the best option under center.
Kaepernick is recovering from surgeries on his right thumb, his left knee, and on his non-throwing left shoulder to repair a torn labrum, which landed him on season-ending injured reserve after he lost his job last fall to 2011 first-round draft pick Blaine Gabbert.
On April 1, Davis posted on Twitter: "Dealing with Trent is giving me a headache."
"I can't get into what his feelings are. I've not addressed them directly with Colin," Baalke said. "That's just not something that we've done at this point."

Gabbert took over in November for the benched Kaepernick, who completed just 59 percent of his passes with six touchdowns,Andre Johnson Jersey, five interceptions and a 78.5 rating before losing his job. Gabbert said when the team's 5-11 season ended that he expects to be the starter in 2016.
Also Wednesday,Wholesale Authentic Jerseys, Baalke said retired 49ers right tackle Anthony Davis wouldn't show up to join the team until he has been reinstated to the NFL.
Baalke and Kelly are eager to see — if Kaepernick does indeed stick around, that is.
"I'm not going to get into our conversations within the media. We've had several text messages back and forth and that's the extent of the conversation. There's nothing more to add to it than that," Baalke said. "You have to ask him. It's voluntary (offseason program),Armani Watts Jersey, No. 1. And he's not a member of the National Football League, No. 2. So he can't show up until he gets reinstated."
"I think you have to know all the circumstances that go into it, and I'm not going to get into all the hypotheticals or the circumstances surrounding it," Baalke said at Levi's Stadium. "I've maintained from Day 1, as has the head coach, would love to get him out there and work within this system with this coaching staff. That's not changed. I said that in February and here we are today still saying the same things."
Davis, who walked away from football last June at age 25 following a head injury,Nike Blazer Sale Online, has said he plans to file for reinstatement.
Whether Kaepernick wants out of San Francisco,New York Jets Jersey Sale, Baalke said he wasn't sure. Kaepernick hasn't been available to the media despite multiple requests.
While Baalke has been in touch with Kaepernick, he said Wednesday they haven't spoken in person despite both being at team headquarters. Kaepernick is around rehabilitating from three surgeries and attending team meetings during the voluntary portion of the offseason program.
SANTA CLARA, Calif. (AP) — Trent Baalke is not ruling out the possibility of still striking a trade for Colin Kaepernick, though San Francisco's general manager is adamant he still hopes to see the quarterback working in new 49ers coach Chip Kelly's system.