Well, as long as his papers are good, there's no problem at all. Because it's all in the bloodlines, that's what's really valuable, not the specimen that you have at hand. That's just a coincidence. Never mind that he has only one leg! That's only a small hiccup in the heritage, two generations down the line and you won't see a thing anymore! As long as he has a fine paper trail, he's fit for the job.
And next to that; one legged horses nowadays really are the Thing. Every top dressage rider goes for one leg only. They have much more impressive gaits, much more room in the shoulder and they have longer suspension moments because they don't have to bother with all the other legs anymore. And imagine how that leg will stretch out during extended trot! Very flashy. Bound to make every dressage-judge drool!