Okay, that's just a mess. It does sound like they were trying to have it both ways, which I guess is what you'd expect from a gimmicky storyline where they "kill" a character that everyone knows is going to come back before too long. Of course it's all a fakeout, he's not really going to be killed off, but they want to pretend the story actually means something rather than just being a gimmick, so they come up with a convoluted explanation for how he really died, honest and for true, even though in practical terms he kinda didn't, since, hey, he's still here!
Anyway, I never read the actual comics, just the novelization. The book probably streamlined things a great deal.