The Molecule Man (who had stored the energy of the Beyonders), reset time before the Incursions (after Vic learned his lesson), and everything progressed normally from there. Not a reboot like Flashpoint, just a time jump to a couple of "years" before. Now Reed, Franklin and the Molecule Man are rebuilding the Omniverse. Thanos himself wasn't recreated, and was left in a bit of a "ghost" state, outside of the Omniverse, in the black space. When the Ultimates crossed over to take down Anti-Man, he got into the main universe.