As for Shelly... Sigmund is much stronger than her, so he could easily defeat her, then confiscate her team. No one noticed she was gone because no one had the brains on how to get through her gym. As for Fern... Well, he was never there when you actually entered Route 1. See, what happened is that you proceeded as normal with the story after handing Fern's ass to him. You continued to go below the city, where you met El. However, when you lost the amethyst pendant (? I don't even know..), some magical time stuff happened. You leave after finding and defeating El, when you actually fight Fern. But, due to that magical time stuff, it only LOOKS like you fought him on Route 1. That was why the "voice" wanted you to return to Arceus's birthplace again Or something