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.
I wouldn't call it "a mess". It seems pretty straight forward to me. Basically, his spirit was caught between worlds, until his father, in Adventures... #500
, brought him back. Then the regeneration chamber did the rest.
It seems to be one of the more interesting sci-fi resurrections I've seen. I'd wager it is better than Spock's, Trip's, and Carson Beckett's (although, that last one was clever on the part of the writers to use the show's established storyline to pull a fast one).
, do yourself a favor and check out the trades covering the Death/Funeral/Return. They are great, epic reads.