I'd say vacuum it up and 'try' not to suck up your fry. I've had it happen lots of times whilst doing water changes that small guppy fry accidently get sucked up. I just scoop them out of my bucket with a net and put them back in the tank. Is probably quite stressfull, but it doesn't exactly kill them.
You could also place a piece of nylon or something else over the intake of your vacuum. That way the food get sucked against it, and you just hold a net under it once your vacuum leaves the water.
Be creative! I'm sure you'll find a way to remove it
Also, if it's not too much food, it won't have too much effect, since the breeder box is inside your main tank, right?