Very weird that the books are supposed to be 98% canon and yet that tagline is the plot for the first book.
That's not weird. Canon is only canon until it isn't. Even onscreen stories can be erased by later canon (e.g. the "all a dream" season of
Dallas, or
Highlander 2, or all the
Halloween sequels retconned out of existence by the new movie). And "canon" in secondary sources like novels and comics, stuff that has a smaller audience than the main series, is almost always just provisional canon, presumed to be "real" only so long as it doesn't get contradicted. In a case like this, where the books were presumably Thomas's fallback for telling stories he'd originally wanted to tell on TV, it's not surprising that he'd choose to replace the book version with a TV version upon finally getting the opportunity.
Alien Nation did the same thing back in the '90s -- a couple of revival movie scripts were novelized at a point when it was assumed the show was never coming back (though the books were never declared canonical as far as I know), but then it did get revived and the movies were made after all, superseding the book versions.
Besides, canon is more about broad strokes than fine details. The fact that a particular event happened in the characters' lives may be part of the "truth" of the fictional universe, but the specifics of
how that event happened can be rethought if there's an opportunity to retell the story. For instance, the story of how Peter Parker became Spider-Man is an integral part of Marvel Comics canon, but the details of how and when it happened have been updated and reinvented multiple times over the decades. I myself have been trying to sell a novel that expands and reworks my first published story, so that while the overall event depicted in the story is part of my universe's canon, the specifics of how it happened will change when and if I get the novel published.