My theory is that Crono and team clear the Black Omen, and the explosion semi-replicates the Ocean Palace incident and warps them to Lavos in 1999 AD.
That's actually how I always thought it happened to. It's more stirring from a dramatic point of view, too. (The world is doomed, the heroes show up at the last moment to save the day, ect)
But I guess you can get around the paradox with the shell if you figure this--
Time is relative depending on the being. For a butterfly, a day can seem infintely long. To a star, our lives flash by like motes. If Lavos's powers were strong enough, its own reality could cause a sort of bubble, that slows time for it, and makes the rest of history just fly by. So, in essance, no matter where you access it from, you're fighting it in its own relative space. It's not another physical dimension persay, but whenever you travel to Lavos, it's the "present", for Lavos. This could also be what Queen Zeal was seeking, as Lavos's relative space would allow her (and the Black Omen) to last forever, as time for her would be slowed to Lavos's own relative time. And Lavos never gets to truly attack, because no matter where you're attacking him from, you're getting him in his own relative space. Sooo, when you appear in 1999 AD, kill the shell, and then decide to go back to 12000 BC to finish off the Black Omen, for Lavos, relatively speaking, time hasn't passed. When you return to him, you're returning mere seconds after you first defeated him, which is why he hasn't prepared a massive arsenal to kill you with.
The Frozen Flame seems to illustrate this too, as in the Dead Sea, it froze all those Acacia Dragoons. They might not be frozen and dead, but might just be caught in Lavos's relative flow of time--and thus to us look like they're standing still.
AND, this also could explain why in the Black Omen, if you enter the Omen in 1000 AD or 600 AD, when you defeat it its 12000 BC. (I remember I did that once just to see if Lavos would erupt on the present day map, but he didn't. XD) If time inside the Black Omen is relative to Lavos, then it's still 12000 BC inside, no matter what time it is outside. So you actually defeated the innards of the Black Omen and brought it down before time inside had progressed that much further beyond 12000 BC. It sort of "pops the reality bubble". Queen Zeal is probably capable of monitoring what time it is outside, while she's able to stay in her lovely little infinite fortress, where time moves slow enough for her to retain her youth while history flies by in an instant.
...but then when you have that little dude warp you out of the Black Omen if you get tired, does it take you to 12000 BC, or the time period from where you entered originally...? I never warped out--
Oh God, I think I broke my brain. I bet none of that insanity made sense, or I just totally described the pocket dimension. (Wee for unncessary ideas!) XD If I did describe something that's already been said, forgive me--I've read so many articles lately that they're overlapping in my mind. LOL
Anyway, my crazy theories aside, getting around the whole "Lavos died in 12000 BC" thing has been interesting for our project. As always, I really thank you guys for figuring this stuff out. LOL This is the kind of stuff that I miss while play, and I'm completely fixated on fitting the canon as much as possible, so I'd hate to get something this huge wrong. I have figured it out thanks to your musings though-- (It nearly killed me, but I think I did it. Yay for staying true to the canon! And don't worry--it has NOTHING to do with the craziness mentioned above. I'm assuming he WAS defeated in 12000 BC.). Now, to deal with a few
other things...
(Resumes massively studying the insane Cross twists--these make my brain hurt)
