Here's the thing about Regeneration vs. Q Who. The latter happened before the timey wimey stuff in First Contact, so the Federation couldn't have known about the Borg then. Sure, you'd think that altering the past would've altered events like what we saw in Q Who, but if it's true that such things must be fixed by time cops/temporal agents, then maybe that's something they didn't get around to. Also, didn't Q de Lancie say something about Quinn having introduced the galaxy to the Borg in Death Wish? Anyway, time is a river and sometimes I think it just flows over whatever dam in its way and returns to the general route it always takes, regardless of obstructions.