Yes the elder scrolls novel (that revealed these changes) definately shook up the lore, I am interested to see what the 2nd book does and adds to the Lore before the games release.
Unfortunately, probably not TOO much more.
The destruction of Morrowind, collapse of the Empire (it got better...), fracturing/dissolution of the Mages Guild, removal of the Blades from the Empire (quite obvious, since they apparently only have ever served the Septim emperors as they were Dragonborn (Reman dynasty was too, but they were the guys who established the organization that later became the Blades, the Akaviri Dragonguard)), re-emergence of the Aldmeri Dominion, the Argonians apparently taking a few levels in awesome.
Then again, indications are that we'll see the Dunmer on Solstheim, the fate of Umbriel and the Imperial City, the resolution of the Sul/Vuhon conflict, and a lot, lot more.