One hopes so. However, lets say I want to write an article with new fighter powers to submit to Dragon. What am I going to base it off; use the current fighter at-will/encounter/daily system or Essentials "MBA-modifying Stances with no dailies" build?
If you say the PHB one; then the Essentials line is a one-off with no official support going forward beyond what can be interchanged between it and "core".
If you say Essentials one; the PHB fighter becomes obsolete, again barring power-swapping between the two "builds"
If you say write powers for both, you're doubling the chances of something going haywire or someone only using 1/2 of your article.
See?
No... not really. There are cleric articles for specific gods - that doesn't mean all "non-Sehanine" worshippers are not longer supported. It means that one article might not deal with them.
What build should you focus your article around? The answer to that is entirely dependant on what your article is. I'm assuming it isn't simply a 'Fighter' article - most have more of a concept than that. If it is an article for a new Knightly-order, maybe you use the Essentials build. If it is an article about the Gutbuster dwarves, maybe you focus on the Battlerager build.
Or maybe it is a more general fighter article - and yeah, you go ahead and include options for both. The basic Warlord 'Class Acts' article included a ton of feats - some for Bravura Warlords, some for Insightful Warlords, some for Resourceful Warlords, some for Tactical Warlords.
So your generic fighter article might have a handful of feats and utility powers that work fine for all fighters, plus specific options and stances for the knight, and specific options and attack powers for other fighters.
Both can easily be supported without either being sidelined, just like is true of every other class with multiple builds.
Same deal: I'm writing a module for Dungeon. Which goblin minion am I going to use; the original one in the MM1 (which has been errata'd and rebuilt to meet MM3 standards) or the new, already-fixed one in the MV?
Granted, both are kinda corner-case, as a DM I can mix in whatever I like (I used 3.0 PrCs and monsters in my 3.5 and Pathfinder games too) but the official line forward can't support two "cores"; either PHB/DMG/MM 1 is still the Core and Essentials is a one-off product never to be expanded upon OR Essentials is the New Core and the PHB/DMG/MM lines slowly fades into the sunset.
Again, really weird question here. If I'm using a Bugbear, do I use the Bugbear Strangler from MM1, or the Bugbear Wardancer from MM2?
Answer: I use whichever one feels appropriate to the plot, or caught my eye as an interesting enemy, or whatever criteria I want to use to decide. Neither is a more 'official' Bugbear than the other.
I suspect most enemies in the Monster Vault will again just be different types of enemies of those we've already seen. There might be some weird cases with more unique enemies like dragons.
But asking a purely hypothetical question about that, and trying to use that as proof that Essentials will have rendered the PHB/MM/DMG obsolete... yeah, I don't think so.
In short, there aren't two "cores" being supported. There is one game, and a variety of resources for it. Given that those resources don't contradict or overwrite each other, they are all able to exist alongside each other. The Monster Vault doesn't render the MM1 null and void any more than the Draconomicon did, or the MM2, or the MM3. Other Essentials books don't make the PHB classes 'fade away' any more than Martial Power did.
Future lines and products will continue to support whatever is appropriate. Just like we've seen Warlord articles supporting both the PHB Warlord builds and the Martial Power Warlord builds, we'll see future articles supporting both PHB Fighters and Essentials Knights, and there really isn't any reason to assume otherwise. And there certainly isn't any support for the claim that they somehow
can't support both at the same time.