I never had that feeling. I was absolutely sure that both of them would be on the ship when they arived to Earth (and honestly, they should have been there too).
Neelix stated many times that he would stick with Janeway and the others. Kes was as eager to get to Earth with them too, besides that she wanted to learn and explore. And after "Cold Fire" I was absolutely sure that they would find a way to prolong her lifespan.
The short lifespan was a big mistake, the worst flaw in the character. To be honest, a species with such a short lifespan could never develope into more than primates. Not to mention the error with the "one-child" syndrome. Sometimes I wonder if the writers really did know what they were doing.
Anyway, those errors could have been corrected.
After the 1st season I had a feeling that Kes was not going to end up on Earth. There was way to many flaws with her character. In fairness, all the characters had major flaws the 1st season.
Everyone can have a second chance as they can grow out of their 1st season. Kes, darn it is hard to really move from that problem she has a short life and was already 2 years old with six more to go.
In fairness they never killed her off but really they never settled about that. Last as I recall she was in a ship with a return back to her home. Still I think that was in seson five. That has a problem as she would be well 12 years old and sorry to say she would be older then she should be.