Quick re-cap: Charlie says "I'm not involved with that any more. I did the first draft." Film sites are still listing him as one of the movie's many writers.
Well, listen, man. I have super reliable confirmation from a source that Charlie is listed as the writer on the first draft's title page, in a later draft the title page reads "Original draft by Charlie Kaufman, Previous draft by Jamie Linden, Current draft by Patrick Ness," and that Ness' draft does not resemble Charlie's version at all. (Also, Ness was less than keen on making any changes to his own adaptation of his book A Monster Calls.)
So I'd say we're almost certainly not seeing any of Charlie's work once this one hits the screen, 2 years from now.