To quote myself from an Ammobunker topic:
The nature of time is pretty flexible in WH40K. It's what TV Tropes would call a Timey Wimey Ball - those rare cases of 40k time travel have few consistent rules; after all, it's the warp!
Paradoxes are not unknown, from the stable Ontological (ships being sent to answer their own distress signals) to the unstable Grandfather (the Ork Warboss who killed himself to get two of his favourite gun)
The above-mentioned Grandfather paradox averted a Waagh, so clearly timelines can change - or at least exist in multiple forms.
However, deliberately going back in time to change things is a no. Time travel is something that only happen on a very rare and entirely unpredictable basis - or at least should only happen on a rare and unpredictable basis.
The moment you introduce stable time-travel to the setting, other than perhaps as something Tzeentch does for giggles*, the time-line is doomed to fall apart.
Ships going back in time unpredictably and the rather unreliable Emperor's Tarot... these work fine, but if you can get in the TARDIS and think "Hey, I'll go kill Horus before he starts the Heresy", the setting suddenly makes no sense.
I am writing a character who made an (unexpected) jaunt back in time, but I plan on treating her future as a possible/parallel one (where she only knows the crudest details of how it came to be that way), thus saving a lot of the potential mix-ups and paradoxes.
* That said, I did once write a plot somewhat inspired by the Terminator films, where a Daemon figures out how to re-emerge in the past and goes about trying to kill someone who'll thwart him in the future (particularly the second film, as he/she/it kept possessing different bodies to disguise itself).
The protagonists in said plot were there partly through luck, partly through hefty doses of prophesy... and were expected to work quite hard to keep up and work out the details behind what the daemon was doing.