The Omega Sanction was established in Seven Soldiers: Mister Miracle as a sort of trap, an infinitely nested series of miserable alternate lives. This was sort of a retcon, since before it was just assumed that Darkseid's Omega Beams just fried your ass.

At any rate, Batman was shown alive in the last issue of Final Crisis. Well, it's a shirtless guy in a cave, and his face isn't shown, but he puts a yellow utility belt down and he casts a Batman-shaped shadow, so it's pretty clear—it's actually the most obvious bit in the whole damn issue (Grant Morrison has a bad habit of packing too much stuff into the end of a big storyline, so narrative cohesion goes out the window and it ends up reading like a highlight reel of what happened).