Almost certainly, Joss decided to start all over again with his "After The Fall" series in order to make a series that would establish a (more or less) canon continuation of the series the way that he envisioned it. I don't think that anything past the "After The Fall" arc is considered canon, since Joss had little or no input into what happened beyond that point. If you take the final scene of IDW's "After The Fall" arc and go directly from that point to where he crashes through the "Hollywood" sign in the Season 8 flashback showing his first contact with Twilight, I think that that's the point at which Joss connected the two series. Of course, if that really is that case, then it would appear that Angel was the only one to escape from hell, and everyone else, including Spike, is still there. Or maybe we just aren't supposed to notice that.
Then again, maybe I've figured it out all wrong.