You mentioned he keeps sniffing... That sounds as if a scent might be frightening him. Has anything new been cooked or eaten or burned? A bew scented candle? Your son using a new deoderant? ANYTHING? Some cats are very sensitive to smells (we tend to think more of dogs, but cats live in a world of scents too) It may not be anything you would consider scarey, but scents are strong emotional triggers in all mammels.

Keep reassuring him and encouraging as you are...

poor kitty! and kind you for working with him.