Every thing Kes experiences going backwards also has to happen exactly the same going forward. Any changes no matter how small, creates a new timeline.(isn't that how they also explain in in "Deja Vu" w/ Denzel Washington?)
In "Before & After" the Doc says that Kes is jumping back in time due to her being exposed to the Kronoton radiation from the Krenium torpedoes, so Kes still needs to be on Voyager going forward to still be exposed to that radiation. The Doc clearly states that her exposure to it is from their past.
So because Kes encounters Species 8472 and leaves Voyager BEFORE the YOH, she is now never exposed to the radiation that would have caused her to travel backwards in the first place. Which means everything BEFORE or AFTER that Kes tells the crew about the YOH and the Krenium become a whole new timeline.(If you're a fan of the Avergers comics, then you'll understand much of this due to the villain Kang. B&A and YOH are both stories adapted from that concept)
Proof is, Seven taking Kes' place in YOH and discovering the torpedo frequency instead. If Kes actually had experienced all that, even if the crew forgot the computer wouldn't.....unless it never happened.