I don't really my the continuity problems from 'Regeneration'. Mostly because I consider the ENT timeline to be an AU created from the effects of FC. Time travel was used to rewrite established history. Similar to what we see in ST09 with Nero and Spock.
I had wondered about this during first run, especially with all the "Akiraprise" business being thrown around back then. It would have been a believable way to go in my opinion. In fact, I initially thought that was what the whole Temporal Cold War thing was setting up.