The Blood Angels will wage vampire war on the werewolf for some reason or another, or they will avoid the cliche like the plague.
As for plot, I agree with the 10,000 years sentiments. The backstory/plot really is a description of the status quo that provides the backdrop for the much smaller plot threads to exist. Major 30k plot changes don't really have to impact 40k at all. You've got 10,000 years to get back to the 40k universe, and that's a long time frame to fit a lot of story, or a lot of retcons, whichever works.
The other thing to consider is that what is "known" about the history of 40k is largely from Imperium Propaganda, tradition, and zealotry. The games and lore of the 30k are the "truth." 10,000 years is a lot of time to indoctrinate the Imperium's version of that truth. 40k history is a revisionist history, whereas 30k is the actual event. The two can conflict without resulting in any real contradiction, or one time's story really driving story changes in the other.