I always thought that the AT Triforce cloned itself at the end of OoT, so that there was a total of three Triforces running around: AT Triforce, which had the Courage part split by the leaving of Link to the CT, the Wisdom part split by Daphnes at the Great Flood, and Power kept by Ganon in wherever. AT Triforce Clone, which was brought back to the past versions of it's former bearers and was used in TP and other games where the Triforce was split, and CT Triforce, which was used only in the IW and LTTP.