Well, Battle for the Abyss takes place almost entirely while in Warp transit and spends a lot of time over how screwed up it can be. Unfortunately, the story doesn't contribute to advancing the HH, but does demonstrate that not all the marines from the Traitor Legions were traitors.
I beleive one of the earlier Gaunt's Ghst novels contains a portion of fighting in the Warp while in transit to another star system. Rawne certainly deals with very nasty case while keeping Gaunt's son alive, and his prisoner safe. I'm uncertain though which one it is if any of my fellow Heretics can recall.
One of the main characters of ADB's Night Lord's series is a Astropath and so deals with the Warp quite a bit. What makes it interesting is that she is a Astropath in the service of Chaos which makes using the Astromonicon (or however you spell it) an interesting task.
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