Annorax stopped the Borg? That's a big stretch.
Seven of Nine was not on Voyager in the Before and After Timeline/episode.
Borg space was either shaped different, since Before and After was both a month away from Borg Space and Borg Space was inbetween Before and After and year of Hell, or not there at all.
No Borg, no 8472. Or at least, they stay in Fluidic Space.
If Kes meets 8472, she turns into a god and leaves, so there was no 8472 in the Before and After Timeline/Episode, so the Borg did not exist at that local in timespace, or at all.
However!
The Borg are not temporally Inert.
If you found their point of origin, then the Queen, centuries earlier, in First Contact targets another planet with her interplexing beacon, or those two drones from Enterprise chose a new home world to go home to.
Annorax can change the shape of Borg Space, by changing which planets/cultures it assimilates, but out right destruction might be impossible since there are thousands of Cubes on time travel missions, and Queens are omni temporal... They can register multiple timelines simultaneously, both of which plays havoc with Annorax's weapon.
Maybe because Janeway wasn't there, Chakotay betrayed the Borg early on and he murdered Seven of Nine like he almost did in the prime timeline. Although "The Borg assimilate civilizations, not individuals", so Captain Chakotay's Voyager should have been totally safe bisecting Borg Space for years, as long as he didn't do anything stupid.
PS
Krenim Qomar (the Planet from the episode Virtuoso, with a Krenim Flag planted in it's bosom.) is 25 - 35 thousand lightyears from Season 3 of Voyager.