A really big retcon would be, when they eradicate everything that happened in The Dragon Knight Saga in favor of a more Sourcefocused-story.
Did they really eradicate it? I didn't think DKS was at odds with the other Divinities, just that it was a particular tangent in pursuit of Divinity's "main quest". It's just one that focussed on Champions and Dragon Knights and so on rather than Source, but that doesn't necessarily diminish the significance of the latter.