He's eating in the hole, just not down below.
I would say as soon as you can, take the food out of the hole, and have the smelly food down below. It would be awesome if you could lure him to a room and close the door so he wouldn't go back up there, but I'm not sure how you could do that..
I think he needs to learn now that if he wants food, he's going to have to come down for it (unless of course a day goes by without him eating at all - it's too dangerous for a cat to become anorexic).