Are they just discolored from sun? Or it looks like a few spots, maybe bleached from drops of something?You can always dye or paint the cones, but that will change them. I know that's the problem you are worried about. The obvious answer is to recone, but that's not real cheap.
I suggest calling David Miller at Speakerworks (800-526-8879) and ask him. If anyone will know how to make the color uniform, it would be him. I'm afraid the only way to do it right is to recone, but it can't hurt to ask. He won't tell you "recone" just to get the business, in fact, sometimes I want a recone and he suggests a less expensive repair instead. So give him a call and let us know what he says.