Yeah, she changed history so whatever rank or position she held in the pre-"Endgame" future may not be what she becomes in the new timeline. This Janeway won't be going back in time, since Voyager got home 20 years earlier, Seven and Chakotay are alive and Tuvok gets to save his marbles.
Besides, I only recall her being called "Admiral Janeway" in "Endgame" and Star Trek Nemesis
. Is the "vice" bit from the novels?