I feel like it's time that I should say how we are handling the discrepancies between The Secret History of Twin Peaks and the show/movie here on the Wiki. But first, it should be noted that Mark Frost seems well-aware of what he put in the book and that it was all done intentionally. There has been speculation that this could mean two separate universes will be presented in Season 3, but as this is nothing more than speculation, we can't accept it into the Wiki yet.
If this becomes the case, then we'll edit articles accordingly, whether that means splitting articles between universes or creating new sections to make the differences clear. I'll give an example of what I mean by this: Say that Norma Jennings in universe A is significantly different than Norma in universe B. We might create separate articles for the two Normas. If there's only slight differences, we'll keep it all in the same article, but in different sections.
But for now, we should assume what is stated in the show and film to have precedence over everything else in terms of canon, since they are the main parts of the franchise and Secret History is supplementary material. Like with Norma, we are keeping Vivian Smythe Niles as her mother rather than Ilsa Lindstrom. The continuity issue regarding Lindstrom is noted in the Behind the Scenes section, however.
If there are any questions, ask away! I'll try to answer them to the best of my ability.