Sort of. I made major changes to the map in 3.x. The inner sea is much larger, and there are more islands in it (including some large ones). In my 4E campaign, the metaplot of 100 years ago has moved up to only 30-40 years ago. The cause of the problems was that gods from another pantheon tried to move in on the FR gods. They did so by trying to bring the other half of Aebir Toril back, along with their worshipers. Things didn't go as either side in the gods war wanted, and many gods died (or were subsumed by other gods to create more powerful beings for the fight). Some of the islands in the inner sea are the bodies of dead gods.
But, I never used the FR as the cannon realms anyway. And, I don't get the complaints about the 4E realms invalidating the older versions, or being too generic. The longer the FR existed, the more WotC jammed stuff into it that was in the rules, but not in the FR. It was becoming more and more generic all the time.