Kes 1 blows up future Voyager, goes to the past, acts like a crazy person, and gets murdered, while Kes 2 is watching. Kes 1's corpse is stored in the hold. Kes 2, the young Kes from the pilot, 50 days later, lives a life similar enough to Kes 1, records a note for her crazy old person self, and leaves in The Gift. She gets senile, blames Voyager for all her problems, and needs to blow up season 6 voyager to go back in time and save her younger season one self, who is Kes 3. When Kes 2 arrives to kill everyone, Janeway says "dude we love you, look at the corpse we made from killing old senile you 6 years ago, and here's a note from 6 years ago you, who thinks you are dumb, you should stop and she does not want to be saved".
Kes 2 goes Home to Ocampa.
No Kes 3 timeline is created.
We don't know if our VHS tapes, and later dvds were about the Kes 1 universe or the Kes 2 universe.
If our VHS tapes, and later DVDs were about Kes 1 Universe, then after Fury we started following the Kes 2 universe, because Kes 1 murdered all our friends, and everything we didn't see, might have been just slightly askew, so everything should be re-filmed so that we can re-buy the first 6 seasons again for the correct timeline. Is that really too much to ask?
If our VHS tapes, and later DVDs were about the Kes 2 Universe, then it's all cool.
