>>49375937I'd assume people were hunting them more and more as the years went by, and to keep the species around, people started breeding them, eventually releasing them in secluded locations such as kalos' friend safari, various spots in alola, galar's max lair, and sinnoh's grand underground.
alternatively, some turtwig, chimchar, and piplup managed to get to the underground somehow, and when dittos were made, someone managed to bring one to hisui, and ditto had some fun with their cyndaquil/quilava/typhlosion, explaining the cyndaquils in the grand underground