Through the flank??
A colt of ours was just gelded on Thursday (5/27/10). The doctor went through the sheath area into the abdominal cavity.
If the "missing" testicle was passed through the first ring and into the inguinal canal and trapped there, then yes, they can go in through the sheath area, but if the horse's testicle never descended past the first "deep inguinal ring" and is still residing in the abdomen, it's typical to go in through the side to remove it. This is currently what is trying to be decided with my yearling colt Finn - his second testicle is in the canal - trying to decide to wait and see if it emerges or go ahead in after it.