Obito isn't talking about kamui, he's referring to the right side of his body and his left arm being made of the first hokage's cells, meaning if Itachi knew this he would have made sure amaterasu hit the part of his body that wasn't clone material. I think when he jumped backwards into the shadows he ripped off his right arm, then quickly regenerated it.
EDIT - It was Obito's left hand,not his arm.