There were endless moments in season 3 that would have been solved by reaching out to the progressive Borg collective from the season 2 finale. Not to mention that a few character arcs and character development moments that just seem suspiciously absent in season 3. So, is the entirety of season 2 not cannon or am I missing something?
Not retconed per se, they just can't make their mind up on what the series is and keep radically changing direction and dumping prior development and characters. Changes are often for the better and don't directly contradict but there's certainly a lack of any common thought in the story they're trying to tell.