I very much like the idea of the current timeline being ancient history, it makes everything taking place seem that much more interesting to me, gives it more of a Horus Heresy feel.
Yeah, it's actually strangely compelling to write in a time other than the "present day".
I haven't done it too much before though. Going backward makes it pretty easy to be anachronistic - for the example I normally use, the first Eisenhorn book starts in 240.M41, but mentions Tyranids (Tyran isn't destroyed until 745.M41) and Amalathians (there's no exact date for the conclave on Galthamor, but it spurred Lord Macharius' crusade, so is almost certainly between his 386.M41 inauguration and the crusade's start in 392.M41) - and going forwards doesn't really mean a lot unless you can fill the gaps in.
Jax's unique perspective is a very useful tool for that. It's already been touched on but, as will become more apparent later, her mind just doesn't work like a normal human. Her mutation's approach to not ageing is often rather literal - her memories don't (and can't) fade with time. She can recall conversations with Inquisitor Skoll as well as she can recall the ones she had with Rae yesterday.
This leads to a very unusual perception of the passage of time. Her memories don't ever feel "old" to her, but she can also remember every single day in-between.
So sometimes the way she thinks about time is like a twenty-four year old (for example, a year still feels like a long time to her*) and sometimes a twenty-four hundred year old (because she really can refer to things that happened that happened in the millennia before last).
* Which is possibly why she hasn't become completely detached from mortal humans. While she far outstrips a normal human lifespan, even with rejuvenat, it's still a long time to her. (Fairly unusually for an immortal character, who tend to start using comparisons with mayflies). However, more on that later in the story.
Good stuff and here's hoping the next instalment doesn't take another year!!
Hopefully not. A lot of the later story is actually rather well drafted out, and I'm starting to get more assertive about filling in the gaps.