Actually, the answer is quite interesting. He was in the movie. He's the main character. -No, that was Nicolas Cage! Well yes, Nicolas Cage was the actor in the movie. But this is the guy he was portraying. Yeah, that's Charlie Kaufman. In the flesh.
To me, they hardly even look like the same person. Wasn't he self-described as fat and balding? The real Kaufman doesn't look that way, not to me. And we all know that he doesn't really have a twin brother--that was just a creation for the movie.
So my question is: how much of this movie is based on the real life of Charlie Kaufman, and how much is just made up?
There is an interview with Susan Orlean in which she says, "I did have real concerns that people wouldn't understand what part if this was real and what wasn't." She seems to suggest that most of it is real, but that at some point in the film, it turns fictitious. (You can watch the entire interview if you would like:)
So I guess we'll all have to go find Charlie Kaufman, befriend him, and figure out the truth! I know that I don't really have an answer. Sorry guys. :P