The main fluff change I found was in the Galactic Map at the end of Appendix 1. A whole series of places have been moved around, some quite extremely.
I was never that up on Galactic geography, but I swear the Tau Empire was south of Macragge, not north. And wasn't the Storm of The Emperor's Wrath in Ultima Segmentum? Now it's just east of the Gothic Sector. Badab is also much closer to the Maelstrom than I remember.
The position of the Necron Crownworld of Mandragor (home of Imhotek) has been placed... and it's slap-bang in the middle of Hive Fleet Kraken. How they survived that and left enough 'Nids to threaten the Imperium I don't know.
They've also put a massive (wider than the maelstrom, and longer than the galactic core!) "Astro Telepathic Duct" over the North East, without any explanation of what it is, why it's there, or how it was built. Anyone have any ideas as to what I'm looking at?