My trick to avoid paradoxes by chrononauts or time-travelers is the characters can't change the past because they really they go to a parallel earth, a time sphere, something like the hollow earth from Mystara. And if a timeline suffer many changes, then the alternate timeline doesn't disappear really but it becomes a special type of demiplane, a kingdom of dreams (or nightmare), where fay lords are more powerful but planar barriers are weaker to stop invasion of creatures from the Far Realm.
I imagine the crystal sphere of Nentir Vale like a solar system with some worlds, and these has their planar gates with other D&D (and Magic: the Gathering) worlds (Grayhawk, Dragonlance, Mystara, Birthright). We could say I imagine Nentir Vale like the d&d version of Stargate SG-1 with a piece of the teleserie "Sliders" and the battleworld from the last Secret Wars marvel comics saga.