Evil Dead
If I recall correctly (been a few weeks since I saw Reloaded last) the architect informs Neo that Zion has already been destroyed......also at the end of the movie I believe we hear that the man on the table next to Neo was the only survivor...........and I could swear I remember Niobe dying somehow inside the Matrix suddenly as if the Logos had been destroyed and her mind/body had been separated (much like Apac and Switch) or something, but don't quote me on that one............yet in Revolutions we see the war going on in Zion and Niobe is alive.