I just finished watching this episode. Very good episode. Jane-way used the Voyager to destroy the time weapon ship thus restoring the time line. The time line however was only re-arranged to allow the Voyager safe passage through the region.
The time weapon ship had not been developed at this point based on the end where we see Annorox at his desk working on his calculations when his wife walks in. So it's obvious that Voyager altered the past only slightly. The eventualities of Annorox's time line still come to pass where billions of lifeforms are erased from history altogether.
One aspect that is unsettling is that Annorox mentioned accessing the Continuum several times. Could Annorox have been from the Continuum and was toying with Voyager much like Q enjoyed toying with Picard? Annorox did mention that time had, emotions thus suggesting a personality.
I seriously doubt that the Continuum would allow a sentient biological species to eradicate countless worlds and species. If those worlds and species had been in contact with another member from the Continuum, wiping the species out could very well have wiped the Continuum out due to a cascade failure of the Continuum do to interaction. Interactions between the biological species and the Q and the Q with other Q. With the time line being restored, the Krenim should still have the ability to use the time weapon ship against the Alpha Quadrant if and when the Krenim find the Alpha Quadrant.
But, in Endgame ,an event that takes place after Year of Hell, Voyager encounters a Transwarp Hub. After destroying two Borg Cubes, Voyager investigates the hub. During the few hours of interaction with the Borg it is very likely that Borg, at some point accessed the data banks of files and downloaded the files to the Collective. Most likely when the Borg Queen came to visit Seven.
While searching through the data files of Voyager the Borg would have undoubtedly have come across the interaction between the Voyager and the Krenim. The Borg investigate the Krenim and discover their temporal weapons and shielding. Without the Krenim knowing where the Borg homeworld is located and their time time weapon ship unable to be used to erase the Borg from the time line, the Krenim and all of their technology are assimilated by the Borg.
Technology that would involve being able to erase Starfleet from the time line while at the same time avoiding changes in the time line due to the weapon being used. Weapons that the Borg can use to wipe the Federation out of the galaxy permanently, without any time line shifts effecting the Collective.