I have seen some fan-based content online here and there incorporating Dune into RT 40k universe, which to me is cool no problem...
This is how I approached it
Arrakis and the whole of the Dune fluff is in the Andromeda Galaxy - some sort of anomaly jaunted Humanity there and thus no record or such...
If/when introduction of that caste is desired - well they are just arriving to the halo stars from points outside of our Galaxy!
Seeing as they have Navigators, this event (i.e. when they disappeared) could be associated to many varied events from the Thulians to the Haarlock business (House Nostromo)...
Time is not a factor - say they disappeared X-years ago, for them that may have been Thousands of Years ago, but when they arrive now - they just left a few centuries ago - thus time paradox fun!
I only use such inclusion in my campaign like for a one-off encounter or adventure - this by no way plays to dominate the great 40k Lore that comes default by the Core Rogue Trader book.
Anyone else like and use Dune stuff?
Morbid
P.S. this concept could be easily applied to Star Wars - we've received reports of something called the Jedi captain on Solace Encarmine ?! ROTFL
Edited by MorbidDon