I for one have grown tired of throwing out my old books to buy a new set every time some Anti-Monitor, imprisoned god, or quantum AI steps up to bat. I can barely keep up with the changes made to history on a regular basis and sometimes I feel like historians are just winging as they go along.
Look at it from the other point of view: if history was merely an assemblage of time, what would be the point? It'd just be numbers with people on it. This way, you get to thrill at mirroring the thoughts of the God-Emperor, despite our perpetual unworthiness!
Historians have to be students of time as well as history. It is their goal to address parallel universes, doings and undoings, and anyone who attempts to kill Hitler.
Just because you don't see it happen doesn't mean it hasn't happened in some version of this universe or the next or the earlier ones or the ones of which we don't speak. Seriously don't speak of them.
While it is true that across the multi-verse such beings can evoke such multitudes of alterations it doesn't mean these events are lost. Take for example Sigil, it exists outside time and space protected from such beings by our Lady of Pain. Historians have recorded histories that have, have not and may not come to pass.
HERESY!