The new Borg queen in S2, the one that took residence in the mind of Jurati, is from an alternate universe/timeline. She came from the timeline where Seven was president of Earth.
The old original Borg queen that we see in S3 was assumed dead from the virus that killed all the Borg. But in reality she had been in hiding.
Yes, ut the Jurati Borg are apparently permanently engaged in guarding the wormhole to another realm where a giant elder god resides, or something. They've been relegated to the status of a cosmic bung cork.