That's the thing about 40k, though. Even if you move the story forward, you still have all of that story behind you to play in. People play chapters like the Celestial Lions who were wiped out, or Pre-Heresy armies before they were Chaos. Hell, the Witch Hunters codex has an IC that is dead. Even if it's a game of the Grim Dark Future, it's a historical game of the Grim Dark Future. Pushing the story forward doesn't invalidate what came before, and it gives people more to work with when building their own armies.
GW just needs to do it carefully. Don't push it to far. Like I said before, maybe the Golden Throne fails and things are starting to get really desperate, but don't wipe anyone off the map.