Months later, he still had said footage that was not used and that supposedly was not in step with his leftist anti-American, anti-Bush views??
Well, I'm not a movie director, but I don't believe you throw away the takes until the film is done. And fairly often you keep many of them long afterward, just in case. Many films have been re-released as "director's cuts" or in revised versions, sometimes half a century and more after they were first made.
The takes are expensive, and storage is relatively cheap. So why would Moore throw anything out before the film was released?