What Could Have Been - The War Of Souls was originally going to involve an undead army, and likely other factions as well, the team behind the Fifth Age had already started to work on it, but this plan was abandoned in favor of what Weis & Hickman wrote.
Word of God - Margaret Weis herself has stated that the story Raistlin's Daughter (which she herself wrote) never happened. The Appendix that was in the hardcover version of Dragons of a Vanished Moon has been said to be non-canonical by Tracy Hickman.
Strangely, enough, Brothers Majere, a late 80's novel written by Kevin Stein (and thus is the only major work to feature Raistlin not written by Margaret Weis), is considered canon, albeit with some adjusting. For instance, Bast, Lord of the Cats, is described throughout the book as a demigod, even though demigods do not exist in Krynn's cosmology. Later campaign supplements describe him as a Beast Lord, with rulership over all felines on Krynn and power exceeding all but the most powerful dragons, but no divinity. Mereklar, the city where the book takes place, is placed northeast of the Qualinesti forest and is therefore quite close to many of the events of Autumn Twilight, not to mention Solace, the Heroes of the Lance's hometown, but is never listed on any official maps or campaign setting materials.