Forget it. "Future's End" was just a dumb episode. VGR had a habit of throwing common sense out the window in its time-travel stories and driving me crazy with their sheer incoherence. I had my fill of trying to make sense of them when I wrote
Watching the Clock -- I'm not getting paid to do it now, so never mind.
From
my annotations for Places of Exile:
It seems easiest to think of the entire episode as being in an alternate reality from the rest of the series, or simply to regard it as an apocryphal story, because it is inconsistent with “Before and After” (in that Janeway has no memory of the Krenim despite being told of them by Kes), and because, aside from the inauguration of Astrometrics (which could’ve happened much the same in a different timeline), it has no further impact on the series.
Thus, I offer the following hypothesis: Despite the order in which events were depicted onscreen, I submit that the entirety of Voyager (and thus the 23rd/24th-century Trek universe as a whole) takes place in the timeline seen at the end of “Year of Hell,” in which Annorax’s timeship had been wiped from existence. After all, there is no explicit mention in “Before and After” of Annorax, a timeship, or any kind of historical alterations; the only thing mentioned is that the Krenim exist and use chroniton-based torpedoes to penetrate shields.
So: “First,” in the Annorax timeline, a version of Voyager encounters Annorax’s timeship and destroys it, resetting the timeline back to the 2170s and creating the timeline seen in [DSC,] TOS, TNG, DS9, and early VGR, in which Annorax never invents his timeship. Two centuries later, in May 2374 in the B&A timeline (six months after B&A), another version of Voyager encounters the Krenim Imperium, which does not engage in rewriting history, but is aggressive in defending its territory. A Krenim ship attacks Voyager without provocation, Janeway and Torres are killed, and the B&A version of the Year of Hell occurs. Four years later, a dying Kes jumps back to 2373 and creates the timeline seen in the series from that point on, telling Janeway of her future experiences with the Krenim. Later, in March 2374 (64 days before Janeway’s May 20 birthday), the final bridge scene of “Year of Hell” occurs: Voyager is hailed by a different Krenim ship, one whose commander is more talkative and warns them to bypass their territory. (By arriving two months earlier, they may have encountered the Krenim before their military status had escalated to the point of firing without warning.) Janeway readily follows their advice, because she remembers Kes’s warnings about the Krenim from the end of B&A. (Why else would she so unquestioningly agree to bypass their territory, rather than negotiating for passage as she normally would?)