...This is one of the reasons that I think that we didn't follow the same ship from the same timeline the entire seven years...
I got that feeling too, and more so with Kes in particular, especially after she saw her whole life (and children with Tom) being sent back displacing the original Kes in that episode, who was earlier visited by a future Kes who wanted to destroy Voyager, to later forget that encounter, as well as the possible happy future, to return to Voyager to blow it up, where she's shown a past Kes to remind her which Kes she was way back in the beginning.
Bizarro time travel plots were one of Brannon Braga's pet favorite subjects, and while it was tapped well in things like his TNG script "Cause And Effect", in
Voyager and
Enterprise (when he had the keys to the car), it ended up creating vast continuity snarls due to all the overlapping it seemed to do in the format.
I know I harp on alot about "Deadlock" here, but it was one of the first times I felt the Trek writer's room were flipping the bird to the audience re: presenting us with a consistent universe. I can't invest emotionally in the character of Harry Kim when I've got the niggling feeling that every episode after that point we aren't seeing the same guy we saw from "Caretaker" to "Deadlock" anymore.
It's a bit like Tom Riker. I know they tossed around the idea of killing off Will and replacing him with Tom, but I'm
really kind of glad they didn't, because in retrospect it would have felt like a cheat. 'Replica Harry Taking Our Harry's Place' feels like a similar emotional cheat, except they actually went through with that one.
"Before and After" is a similar cheat, especially when we get to "Year Of Hell" and none of that shit goes down the same way. And then YoH turns out to be a reset button anyway.