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Am I correct that 6th edition changed the 13th Crusade from a finished (more or less) war to an ongoing conflict?

Pretty much, it's now a stalemate over cadia, chaos owns 50% of the planet, but can't get more ships there for whatever odd reason to support because the IG own the skies but for some equally odd reason don't shell the gak out of the planet.

Where is the best source for current 13th Crusade fluff?

Likely the Chaos dex unless FW's put something out recently.

From ADB:

The 13th Black Crusade has only just been declared/is building up to being declared in current 40K lore, and it's been that way for a while. The store campaign lies in its grave, and my fingerprints are nowhere near the murder weapons.

Also. didn't the event occur before 5th edition came out, so wouldn't it have been 5th edition that killed it?

Where is the best source for current 13th Crusade fluff?

The Black Legion supplement, definitely.

I agree with jareddm, the best source is the Black Legion supplement.

The crusades have essentially been characterized as Abaddon either probing defenses or using the massive attacks as misdirection. The Pandorax book is a great example.

The 13th crusade is probably just another misdirection. Tie up a large section of Imperial power, while sending various strike parties out to capture certain personnel or artifacts.

13th Black Crusade started in 999.M41

The game is currently set in the year 999.M41 or earlier, not Later.

So yes they retconned it, but only because they decided it has not happened yet. Same issue applies to Eldrad's death.

From what I understand is that the 13th Crusade is still on going and has not finished. But yeah that world wide campaign that was to change the 40K universe depending on the outcome never happen because GW could not take the public backlash. Even the Zeist campaign is not part of the original fluff because in the campaign the Tau added the Empire and fought the force of Chaos. But the results from the campaign were so close that it was a minor victory for the Imperium, but for the first time in 10 000 years Chaos had occupied Imperial worlds and managed to gain a small foot hold in the Empire.

But sadly with a push of keyboard buttons all the cool stuff from that campaign is no more

Here's what's gonna happen with the 13th Black Crusade (this is my theory of course, not official canon.)

It will never be fully finished.

On a GW standpoint, authors of the fluff of the universe have stated that the fluff is merely a backdrop to the actual game. There have been few instances in which they mention what could happen, but it will never progress further than 999.M41. This is why we're getting more Horus Heresy material and the like. Once the fluff people finish writing the details of the Heresy, they will most likely turn to other major dates like the Age of Apostasy and the time between then and now.