There are slight differences there. In the case of the BIONICLE movie novelizations, stuff was added in to help clarify things that were omitted in the movie or to help get the book to the right length. There were certainly instances of things in those books where they were based off old scripts, and things changed later.
In general, if a scene winds up on the cutting room floor, though, it is not considered to have happened. Otherwise, it would be mandatory that you watch deleted scenes to understand what happened in the film.
In this case you are dealing with a contradiction between versions of how the Shadow Toa got defeated. One is accurate, and one isn't.