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I'm looking for a good place to look up fluff on time after the heresy up to current Codex Fluff. I would like something that discusses the relationships between the different chapters. So wheres a good place to start?

http://wh40k.lexicanum.com/wiki/Main_Page#.UQwoqr9EHGE

The go to place for easy to access 40k lore. Though always make sure to check the sources cited, as on occasion something gets lost in translation. That said it's still leagues better than the 40k wiki.

tyvm bookmarking it now

I do believe the book Flesh of Cretacia is set a couple centuries after the Heresy, which should fit your timeframe quite nicely.

Awesome I've been looking for some BL stuff for between Heresy books

In the same vain, Battle of the Fang is about the Space Wolves only a few centuries after the heresy.

Here is an online copy of the Index Astartes articles as GW used to print them in White Dwarf years ago. Quite an interesting collection of Marine fluff, going deep into things like Chapter history as well. Maybe this helps with the research, too.

jareddm wrote:http://wh40k.lexicanum.com/wiki/Main_Page
The go to place for easy to access 40k lore. Though always make sure to check the sources cited, as on occasion something gets lost in translation.

I think the bigger problem is that this wiki attempts to merge sources that simply may not have been intended to tie into each other in the first place. Readers can easily walk away with an individual editor's personal interpretation believing it to be some sort of "truth", rather than forming their own.
My own advice would be to not only check the sources cited, but actually prefer them to the article itself, basically using Lexicanum like some sort of index. Although some articles are indeed 1:1 copies of their respective source rather than a mix; I'd wish that was more common.