"Phantom Sense", by Richard A. Lovett & Mark Niemann-Ross, published in Analog Science Fiction and Fact, November 2010.
It's got all the elements you describe. Ex-soldier:
Kip is a former member of the CI-MEMS, an elite military group
Who uses insects to collect data:
scientifically modified with tattoos allowing them to communicate with and control implanted insects to spy the area around them
Losing them is like losing a limb:
The hazard is, the Sense, as they call it, can’t be turned off and once you’ve had it, it’s hard to let go.
And he gets them back to save his daughter:
Then one day, [his daughter] disappears. ... So they track down the company making [the bugs] and the vendor who provided them to the ex-boyfriend and then trace him in order to rescue her.
Here's the entire detailed plot summary from TangentOnline.com:
Kip is a former member of the CI-MEMS, an elite military group of men who have been scientifically modified with tattoos allowing them to communicate with and control implanted insects to spy the area around them, both seeing and listening in on whichever targets they choose. Sent into the most dangerous areas, lives constantly at risk, the CI-MEMS bugs are indispensable tools allowing them to sense danger before it happens and respond accordingly. The hazard is, the Sense, as they call it, can’t be turned off and once you’ve had it, it’s hard to let go.
Forcefully retired, due to health concerns, Kip finds himself isolated. His wife has divorced him. His daughter hates him. Yet still he can’t resist looking in on them to see what they’re up to. Having discovered this long before, his daughter, Cora Ann, loves to taunt him with activities she knows will cause him concern, comments hurting his feelings and whatever else she can do to get back at the father who was never there. She even dated another former CI-MEMS from Kip’s team.
Then one day, she disappears. Convincing his ex-wife to relax the restraining order she has against him for an unfortunate incident involving a flashback to combat, he teams with her to track down their daughter. The ex-CI-MEMS she dated has somehow gotten CI-MEMS back from a non-military concern. So they track down the company making them and the vendor who provided them to the ex-boyfriend and then trace him in order to rescue her.
Switching back and forth between Kip’s memories of combat and his life now, the story moves at a nice pace and is full of suspense and good characterization. The science is fascinating and a tie-in science fact article by the same authors follows the story, explaining how close the CI-MEMS technology is to being a reality.