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?
There's nothing contradictory about the seasons, and they were written and filmed back-to-back. There's no need for a retcon.