Shortly before Kes left with her new powers, Kes warned the crew about the Krenim and their use of temporally based weapons. But when they reached Krenim space a few episodes later to start the Year of Hell, they acted almost as if they hadn't even heard of Krenim and it seemed as if they had done nothing to prepare themselves. What happened?
At the very end of "Before and After", we have the following exchange:
JANEWAY: Tom's right. I think we should all leave the future to the future.
TUVOK: While I agree it would not be wise for Kes to make all of her experiences public, a report on anything she knows about these Krenim might be useful.
KES: I'll get started right away.
JANEWAY: Hang on a minute. I didn't mean now. Stay and enjoy your party.
This dialogue occurs after Kes' last time jump. While she did spawn multiple timelines, it seems that the timeline that we are following up to the beginning of the "Year of Hell" episodes is the one in which the above dialogue occurs.
I believe it is much more likely that Annorax's timeline adjustments in "Year of Hell" itself are responsible for erasing Kes' contributions to Voyager's preparedness. Remember, "Year of Hell" begins with Annorax's temporal interference, before we are shown the Voyager crew. The very first scene of "Year of Hell" is:
OBRIST: Temporal incursion is complete. All organisms and man-made objects have been eradicated.
ANNORAX: Probe the continuum. Has our target event been achieved?
OBRIST: Negative. Negative target event. I don't understand, sir. We spent months making these calculations.
ANNORAX: Time is patient, so we must be patient with it. Eradicating a single Zahl colony wasn't enough for a total restoration. We have to work on a larger scale. Take us to the Zahl homeworld. Prepare a new set of calculations. We must erase the entire species from time. Every lifeform, every molecule.
So rather than Kes' multiple timelines being the source of the problem — between "Before and After" and "Year of Hell" we are in a timeline where Voyager has Kes' knowledge of the Krenim — the problem is more likely to do with Annorax's creation of multiple timelines, just prior to the events seen in "Year of Hell".
Lore aside, it's more likely that "Before And After" was plugged in as a filler episode after the Year In Hell plotline was conceived.
It did feel like a rushed attempt to wrap up Kes's storyline and character development before Jennifer Lien (who played Kes) was transitioned off of the show. It does appear that the actor/character who would be 'replaced' by Jeri Ryan (Seven of Nine) was still in the air right up until the production of the Year In Hell arc. Google search
seven of nine replacing kes brings up a bunch of interviews from cast and crew on this subject, mainly that it's clear there was a scramble to decide which character could be sacrificed based on viewer ratings. This would explain the lack of Voyager's heed to Kes's warning.
That said, it's perfectly logical that the crew would not be taking Kes's version of the timeline she experienced as an absolute depiction of future events. Think of the alternate parallel universe in Deep Space 9 and how completely detached it is from the original timeline in the show.
Or what has already been said above re: Annorax's temporal interference.
Or maybe the timeline we are seeing in The Year In Hell is simply not in line with the universe that "Before And After" exists in altogether (Star Trek has pulled this before).
This is discussed within the episode itself. Although Kes was ultimately able to return to Voyager, her actions in the past are likely to have spawned multiple timelines. Each earlier jump either erased those timelines or pushed them into alternate (and inaccessible) realities, similar to those experienced by Worf in TNG: Parallels.
TUVOK: Fortunately, Mister Neelix, what Kes has been describing is merely one possible future. On each occasion that she jumped to a previous time, her subsequent actions most likely altered the future from that moment on.
Since, after explaining the dangers of Krenim space to Janeway she subsequently underwent further temporal shifts backwards in time, the timeline with the warning may have simply been erased.
I believe I have developed plausible theories as to how we can follow the "before and after" timeline while still encountering the "year of hell" part 1 where Janeway and crew appear to be unaware of the Krenim. I'm seeing a few possibilities as to how this could occur.
Firstly, the end of "before and after" dialogue strongly gravitates towards keeping the future unknown and living in the present. The only exception to that was Tuvok's decision for Kes to make a report on the Krenim. I can see a plausible scenario where either the crew or Kes (during ascension) consequently decide to erase their memories of the Krenim and the destruction they had on the crew (in order to live in the present and not dwell on the deaths of Janeway and others).
Scenario 1: The crew agree to wipe their memories of the Krenim and rely on a time-released report (the one Kes is instructed to make) to reveal itself within Voyager's matrix a reasonable time before the stardate of the encounter (year of hell). In this scenario, Kes later ascends and either a) doesn't account for the much earlier Krenim encounter when she throws Voyager 9,500 light years ahead or b) Kes correctly accounts for this closed gap in time but doesn't account for Voyager's earlier arrival in that region of space where perhaps the Krenim at that time claim a much larger area of that region resulting in a much earlier encounter than anticipated. Remember, Janeway states that she was under the impression that it was Zahl territory when first encountering the Krenim ship, as Seven of Nine had informed her (as per Borg database in the new star chart they devised).
Scenario 2: This scenario accepts that the crew did not erase their memories of the Krenim. Instead, it was the scientists in the previous episode "scientific method" who decided to erase the crew's memory of the Krenim. Perhaps it was a prime directive of theirs to not allow knowledge of future events. They were incredibly secretive about their objectives and goals. I don't even recall them stating the name of their race. They did state that they already knew Janeway's intentions and that she would kill for her crew. This definitely suggests a plausibility for reading and perhaps altering minds. Perhaps they were somehow related to or allied with the Krenim. After all, as far as we could see, only a few Voyager crew on the holodeck were even aware of the Krenim at the end of "before and after".
Scenario 3: Just as Kes's knowledge of her past began to populate within her mind after she was cured of time skipping, perhaps the knowledge of future events degraded or disappeared from everybody else's. Kes states toward the end of "before and after" that she can now recall events that took place in her past, of which she was previously unaware.