Before Dark Oak transformed into Final Mova, he had sent out a wave of energy that destroyed the entire fleet that was present. But what if that was only part of the Metarex that came?
A Metarex space station appeared in the episode "Hedgehog Hunt", but it wasn't shown anywhere else. It's possible that it could have survived, and the remaining Metarex are harboring there.
My theory is further strengthened in the Japanese version of "So Long Sonic", when the spirit of Dark Oak tells Sonic, "Next time, our descendants will fix the future."
(On a related topic: in comparison with an earlier part of the dub version of the same episode, Lucas is shown to have learned his lesson. Why would he still be evil afterward?)
Thoughts?