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.
It's also imminently possible you're right, but the Relativity or someone else from the 29th century has been busy undoing the damage such widespread awareness of the future events would cause.
Chakotay's vision of the future was also not the future that ultimately ended up existing. In such a world, the Relativity probably left him alone, as his foreknowledge wasn't particularly useful, and they could simply look at some Starfleet records and see if he ever shared what he knew in a way that would affect the future. On seeing that he didn't, they opt to not intervene.
Meanwhile, Janeway has shown time and time again to do whatever the fuck she wants with the timeline, and Captain Braxton probably relished pulling her in, zapping her memory of those events, and dumping her back into her own time.
All true, but how did present Janeway know where Chakotay hid the cider? That’s the whole point. That last line implies she kept her memories.