Shroomy
Adventurer
I don't think that advancing Planescape's timeline by 1000 years actually changes anything. Factions come and go, various powers rise and fall, but to truely change Planescape you'd have to change the underlying philosophies.
The Unity of Rings, the Rule of Three, Center of the Multiverse and maybe the Blood War are the constants of Planescape. However, changing those completely changes Planescape to something that is not-Planescape.
So on one level, you could do a new Planescape, with all new factions and philosophies, but it's still the same old Planescape, if that makes any sense.
While the Blood War would be problematic, I've seen fan created interpretations of core Planescape assumptions using the 4e cosmology, and they seem pretty solid to me. However, ultimately, I think it is largely irrelevant as I expect WoTC to mine pre-4e cosmology and use bits and pieces they wanted (the appearance of Sigil in the DMG for example). I guess we'll see when the upcoming Manual of the Planes is released.