Where did they all go?
Theory 1: Vernon and them work for Walkie-man and left before Lee got back there. But then why leave all the food? And where would they go? Two of them need constant help according to Vernon, and they aren't the most agile, sneaky, people to survive on the surface.
Theory 2: Walkie-man kidnapped Vernon and Clem on their way back and they all left when they realized Vernon and Brie weren't coming back. But how would they know that? And if they weren't working for Walkie-man, why would they be gone when Lee gets back there?
Theory 3: Walkie-man killed Vernon and all his people to get to Clem. But that room showed no signs of a fight, so he either cleans up his crime scenes better then Dexter Morgan, or he ambushed them as they all up and left. But why would they leave that safe haven in the first place with all that food and protection?
Theory 4: Vernon saw the train and he, Clem, and the others made a break for the train to escape the city. But how could they sneak by a giant herd? And why would they think that's a better idea then staying underground and waiting for the herd to move on?
All seem unlikely as I cannot see them surviving outside of their underground home, or why they would even leave there to begin with. And why would they work for Walkie-man if that's the case?