I imagine that Aether isn't lost. Bahamut was fed with way too much Aether and that's what made him so strong. When he was released and he used his attacks all that aether was set free and the land consumed it over time and recovered quickly.
Just my guess on why Eorzea recovered that quickly :3
As for the twelve.. meh. Can't really bond to them. I would rather have a real Primal (Siren :P) than twelve symbols.