"Before and After" got retconned out of existence as soon as Kes left the ship and became an energy being. Because of that, she never lived her life on Voyager including the Krenim encounters.
Notice how Seven was in Kes' place in getting the reading of the Chroniton Warhead? It was to show how Kes' role in the story now never happened.
They just didn't make it clear enough.