To the point: GW aren't, and won't be, progressing the setting. The 40k universe during the latter days of the Dark Millennium is too valuable an epoch to conclude, particularly where licenced products are concerned. The clock stops at ten minutes to midnight. The end is near enough to taste.
What that means here is that you don't have to worry about what you write being invalidated or impinged upon by GW's material - it won't be, as you're sailing into uncharted territory... and that's surely a good thing.
When you put it like that, aye, it certainly is. I'm a lot more comfortable with the idea that GW will never move beyond that point than I would be if they intended to but not for a while.
Personally I never had a problem with the timeline stopping where it does; I just object to their having said it was going to progress, encouraged Inquisitor players/writers to involve our characters in the 13th Black Crusade and then changed their minds about it afterwards. If they were happy with the eleventh hour setting, they should have stuck with it, rather than roping so many people into an experiment that ultimately seems to have failed. My involvement in Inquisitor peaked around the time of the Secrets & Lies campaign, and at the time most of the Conclave were using that as "present day", so as a result pretty much all of my characters are tied to the very end of the timeline. That does bring greater freedom for stuff written later, but it also puts the onus on us to explain how the Imperium still exists hundreds of years post-apocalypse...after all, if there really is no hope for mankind at the turn of the millennium, then any fiction set much later but presenting the galactic situation in a vein we're familiar could itself be considered a contradiction of the canon.
Part of the problem for me is that a few years ago, someone told me GW already had moved the timeline forward a few centuries beyond the end of M41, when they introduced the background about the Golden Throne failing. Having been out of the loop for ages, I (rather naively) took them at their word and have since been imagining an Imperium that fragmented into isolated star systems, an Emperor truly on the brink of expiring, a drastically shrinking Astronimican, alien races colonising the galaxy, whole sectors losing contact with Terra...an "If you thought it was bad before..." situation, as you said about the 13th Crusade (which I remembered as something of an anti-climax, but assumed they would stand by, since it was all deemed canon at the time). To me, an apocalypse whose culmination could be pinpointed to the minute, or even the year, always did seem rather fast for an entire galaxy...I had no problem believing that even when the Imperium's back was broken once and for all, it could take another millennium or so for the dust to really settle.
In fact, I was quite inspired by the idea of a dwindling, post-Imperial humanity struggling to survive as isolated pockets of resistance in a galaxy now dominated by their enemies. I had all sorts of "where are they now" concepts for any characters of mine who might feasibly still be living through this. To me, the end of the Imperium shouldn't have to mean the death of every single member
of the human species...look how long the Eldar survived after the birth of Slaanesh. Foremost in my mind was the question of how long the Inquisition would be willing to flog the dead horse, before giving up on their role as enforcers of the status quo and looking for alternative ways to preserve some small fragment of humanity. You can't be the Secret Police without a state, but any Inquisitors who outlived the interstellar infrastructure would have a lot more knowledge than most of the Imperial nobility/military/etc and some would surely be in a position to act.
For example, there are other galaxies. Million upon million of them. The existence of the Tyranids proves that at least one of those galaxies can support life, since there must have been something to eat wherever it was they came from, and if there are two places where life arose independently then it seems probable there would be more. If the warp is another dimension then it must be Universe-wide, and if warp travel doesn't have any consistent velocity then sailing to other galaxies shouldn't necessarily take the untold aeons it would in physical space. Failing that, the Imperium has stasis technology. If the long way worked for the Tyranids, why not Inquisitor Cracked with an ark populated by would-be colonists?
This is all just speculation really; I'm not suggesting GW should move into such murky territory. They've spent a long time adding detail to their established backdrop and it works for them. Apart from anything else, the wargaming potential would plummet when the armies started running out. The only thing I really take issue with is the retconning of the 13th Crusade, and then only because they made such a big thing of it at the time and until now no one ever told me they'd changed their minds. I would have been fine with setting Amon Dull way back in the past, if "no canon beyond eleventh hour, ever" had been their official stance when we started writing it. But I hate retconning my own material, and having set it in the theoretical "present" so as to chime with those events, I feel an obligation to stand by those dates. Which is all a long-winded way of saying I agree with Ben - jumping a few centuries ourselves has to be the way forward, at least for this particular story. But for me, that means giving a fair bit of thought to how things must have changed.
Not a rant, just a ramble. If I didn't like the 40k canon as it stands, I wouldn't have spent so many years playing games and writing stories set there. And as for Secret's Hold, if no one else remembers the planet being nuked then fair enough - I still think Mac's post is awesome, so forget I said anything.