What continuity? The DCU is more screwed up(not as bad as Marvel's post-Onslaught) now then it ever was before Crisis the only ones who couldn't keep track of all the different Earths were the Marvel Zombies;)
All kidding aside I wouldn't flush it all, I would just move those things Earth II back to Earth II, etc. etc.
As for Byrne, it's just my opinion but the words over-rated and hack come to mind.