That's the last inconsistency to bother me in the Year of Hell. I think it was a neat and feeling-inducing story, I liked the character backgrounds, the Krenim background and the aftermath, but the writers got too inventive and created a jumble that's trying hard to make sense and still doesn't quite do it. I still enjoyed it pretty much, and in the light of the much bigger Voyager issues including missed opportunities, arcs going nowhere or ending too soon, I think this was handled well with some technological details aside. (One might complain that it was also a missed arc opportunity, but with the just wasted Borg space potential and the rushed Seven of Nine development, the Krenim are pretty pretty low on the list of complaints.)
Still... I have much less trouble with the fact that everyone would forget the warning by Kes (easy to believe) than the whole time travel tangle with that deus-ex machina ending on top (pretty much impossible to believe).
And a nod to the show established history? Are you kidding me, Voyager doesn't do consistency. As soon as something is established, it tries best to run away from it as quick as possible.