Given the considerable difficulties in supposing that First Contact proceeded to happen, in fact, at a minimum the Borg episode has to be pitched overboard.
I don't think so. Not only does ENT survive unscathed, but the beauty of alternate timelines and the fact that they can continue to exist, means that ENT episodes that feature them (Regeneration, In A Mirror Darkly) also can be unchanged.
Nothing has happened to the prime timeline. It hasn't been wiped out or altered in any way. So those episodes that feature characters from that timeline, logically must be able to still happen. Remember, in ENT's time, THERE IS NO DIVERGENCE. The separate timelines - prime, and abramsverse - don't even exist yet.