If you are wanting him to put on weight, I would have thought feeding him smaller meals more often would be the best way to do that - is it worth trying that to see if he will eat that way, might fit in more with his previous free feeding too? Maybe a smaller meal would be less overwhelming for him?
I know it's a different situation but when Sweetie was ill and lost her appetite and weight, our holistic vet advised to feed her more often (so I did 3-4 meals a day as you would for a puppy) and to add fish oil and olive oil to help boost appetite.
Sno is the pickiest of our dogs, the others wouldn't walk away from their bowl for anything but he will walk away, have a cuddle and if he gets scared about something, he does need a bit of coaxing. Appreciate that's not necessarily a route you want to take but I find sometimes I just need to sit with him and perhaps hold the bowl, and he'll eat then. Some would consider me too soft I'm sure, but I do it for him because I know he's a sensitive soul and many days he will eat happily on his own.
I guess you are possibly not at the feeding-in-the-same-room-as-another-dog stage yet? But if/when you are, having another dog around might help encourage him to eat too?
Also, you have probably thought of this, but when was he last wormed, maybe that needs doing?