This is the episode where voyager is fractured into different time periods, some in the past, actually most in the past, and one in the future, each located in a different region of the ship, with Chakotay being able to move freely between the time periods. He's trying to return the ship to a single timeline, recruits past Janeway to help him (with some dialogue essentially foreshadowing Endgame), and manages to do so after dealing with Seska, who's on the ship in her past time period, causing some trouble.
It's a nice episode and a good way to do a sort of flashback/clips episode but also develops some nice Janeway-Chakotay character.
At the end, when things have been restored, Chakotay tells Janeway that he can't tell her what happened because of the temporal prime directive. Janeway then reveals that she knows where Chakotay's secrete stash of cider is located, which was revealed to past Janeway earlier in the episode. Chakotay asks how she knows, and she says she can't reveal because of the temporal prime directive.
The whole thing is done as light banter ... but, are we supposed to take this seriously and understand that past Janeway actually remembers her conversations with Chakotay during their movements between the time periods? It makes sense that she would, as both her and Chakotay were given a treatment that enabled them to cross the time fractures without being erased. If Chakotay retains his memories, shouldn't past Janeway have also?
If true, then in the timeline Chakotay finds himself in, Janeway has known the whole time of the rough plot of the whole voyager series up to season 7. Which would be a huge statement, especially if it's that same Janeway(s) in Endgame. You have to remember that this past Janeway was from before they even got to the Delta Quadrant. Awkwardly, as the whole crew is eventually enabled to cross time barriers, many of them from the past, including Borg Seven, they'd all have some memories of what's to come (though arguably not nearly as many as Janeway).
The only argument I can think of for why past Janeway wouldn't actually have retained her memories is that the ship was restored back to the time of the cause of the fracturing, which was an anomaly of some sort in Chakotay's time, and which Chakotay prevented from happening, and so altered all the timelines affected by the fracturing. Having not thought this through enough, I'm not sure how much sense that makes, or should make. But still, why Janeway's comment at the end ... the only on-screen way she could have of knowing about the secret stash is by retaining her memories as past Janeway.
I’m trying to work this through from the angle of what we learned in SNW S2E3 Tomorrow and Tomorrow and Tomorrow.
Now that it’s reconfirmed that Star Trek doesn’t have an infinitely ever-branching and expanding multiverse (unlike Marvel or DC), we need to consider how a resilient Prime timeline (river of time) would affect how the fractured timeline in this episode healed - and therefore who would remember what.
In the SNW episode, La’an (and presumably Pelia) are exceptions. Others in the 22nd century aren’t aware that key events like the Eugenics War and Khan’s birth have slipped in time.
So, in Voyager, it seems as though anyone in the crew who did not receive the treatment would not have been able to integrate memories from across the fractured timeline and would only have what they knew in the current one.
As for Janeway, it does raise questions about her foreknowledge. It’s also the case that she would know that the major events related to what they experienced was likely, but it could slip by years, and with sufficiently major interventions the timeline might fork. In fact, the future shown in the episode could have represented a fork that would occur if they did not undo the fracturing.
Well, there's one future time period shown in the episode (which was maybe a tad risky or thoughtless of the writers?) ... it's far in the future where they're still in the Delta Quad and Icheb and Naomi Wildman are adults and Chakotay and Janeway are long dead. I think the implication is that they're dead because of the temporal fracturing, but I don't recall if that's made clear.
Nonetheless, that this future time period doesn't occur, given Endgame, implies that you're correct. Not sure if Endgame being caused by Future Janeway coming back in time means you wouldn't see its effects when traveling forward in time from a point before Future Janeway's arrival.
Otherwise, the episode is suggestive, especially given how much of Future Janeway is mirrored in Shattered's past Janeway, that alterations caused by this episode lead to Future Janeway's intervention, even as seeds in Janeway's mind that eventually take root .