If a comparison with DC helps, this is like post-Crisis DC, but on a much smaller scale. Secret Wars itself is the only thing nobody remembers except for this handful of characters (and Doom, Strange, Molecule Man, and Old Man Logan). Everything that happened before it, up to and including the last incursion? Still happened, still canon, and still remembered by everybody.
Oh, and add Loki to the list. Now that I remembered, he also managed to escape the destruction of the multiverse. But in his case, he skipped Battleworld completely. He had his own little adventure elsewhere and then rejoined reality when it was restored.