I was recently rereading the original '80s Secret Wars comic on Marvel Unlimited, along with all (or most of) the other comics that were going on at the time. It's quite clear that, for the people who didn't get yanked off the Earth, there was no discontinuity in their existence at all.
And yet, in the comic, the Beyonder created a planet from pieces of a bunch of other planets...including a suburb of Denver, whence came the new Spider-Woman, as well as two other women who Dr. Doom gave powers (Titania and Volcana).
Then, at the end, Molecule Man takes that piece of Earth, rips it out of the rest of the planet, makes a dome over it, and then sails it off into space to "take it home". At some point Dr. Octopus notices that there's a bunch of stars in the sky, and Molecule Man says that he recreated them all. Did he really recreate the entire universe, including all of its history and continuity, so that (e.g.) the Shi'ar Empire was in the exact state it was before, with Deathbird on the throne, even though presumably Molecule Man had never heard of them before? Or was the rest of the universe still in existence, just "far away" somehow?
Now, presumably, nobody on Earth noticed a piece of Denver disappearing then floating back from space a while later. The new Spider-Woman returned with the heroes, I believe, and presumably the villains turned up again at some point (though I guess I don't recall having seen any of them yet, as of May 1985, apart from the Enchantress who returned by other means). So did the Beyonder just sort of reset everything? The heroes had to return via a transporter thing, so what happened with Molecule Man and the rest of the villains?
(Don't worry too much about spoilers--there's a lot of older comics I haven't read yet, but I did read at least a few series up until the late 80's, and Silver Surfer for longer than that...)