Quite a few events from the original background dont quite tie up with what was known before or collected visions etc. (for example im sure there is a picture of Tarik Torgaddon as a traitor in collected visions somewhere).
The fluff is bound to change over time as we get more depth available from the novels and new dexes etc. I think most of it can be explained away as follows:
I look at Codex fluff as being written from a 41st millenia standpoint kinda like a history book. We can read about events in the Ancient world but as huge ammounts of information have been lost and no one who was around then is alive to tell us about it we dont know exactly how right we got it.
The Heresy books while being written "at the time" are personal viewpoints of people involved and alot of it is all about perspective so not to be taken as "this happened exactly like this, period"
Thats how my brain explains away little discrepancies anyway