i'm loving this falmer are the baddies idea!
here's a HEAP of information by a morrowind-moding-falmer-lore-loonatic (he's made 2 falmer mods, one with vality7)
Given that both of these races, the original inhabitants of Tamriel, have been pushed out of Skyrim,
i'm a out 99% sure they come from the original elves aswell, and weren't the original inhabitants, the elves came over in the mythic area right? and spread out from there, as did men.
imo, i haven't actually seen any proof the falmer are gone, i'm pretty sure they'd want to destroy the nords on skyrim, and maybe they could have some dragons with them?
though, i think the "enemy" could be the nords from atmora (is that spelt right?) no ones know atmora still exists right? and wasn't there a civil war up there aswell? "When the sons of Skyrim would spill their own blood." well, the nords from atmora, if there are any wouldn't be the sons of skyrim, so that ideas flawed.
but falmer-baddies ftw!
there'll probably be some more information in the skyrim link in my sig
You're right that the Nords, at least, believe the Falmer to have been defeated utterly in Skyrim, before making a last stand in Solstheim:
"For at that time the Elves were as damned and near death as ever they had been during the great skirmishes of Solstheim. The Battle of the Moesring was to be the final stand between Nord and Elf on our fair island. Led by Ysgramor, we had driven the Elven scourge from Skyrim, and were intent on cleansing Solstheim of their kind as well. "
From
Fall of the Snow Prince.
This is why the Pocket Guide, 1st Ed is intriguing - suggesting that the Falmer have not been entirely eradicated, but that the remnants have gone into hiding, in remote mountains and caves.
I hope we'll get some more lore on Atmora, but I doubt any threat could manifest from there. It's too cold, too dead - even for Nords.
"The last invasion - if that is the word for two ships, largely laden with corpses, begging to make port - occurred in the 68th year of the First Era. The description of the land these raiders had left changes radically over the years, leaving many to believe that it was gradually dying, smothered by frost. Expeditions to Atmora in modern times describe a place of permanent winter, with little life and no sign of human habitation. Whatever population did not succeed in fleeing to Tamriel doubtless succumbed to the ever-worsening climate many centuries ago."
http://www.imperial-library.info/content/pocket-guide-empire-third-edition-atmora