Board Thread:General Discussion/@comment-5448995-20160114192145/@comment-4651179-20160121010603

What happened is that Miles came to Earth-616 and Molecule Man added an extra relaity-warping to make it as if he had always lived there.

And it does seem like he remembers what happened. That scene from Secret Wars #9 seems to indicate he's recalling what Owen told him (the "I owe you one").