Personally I never feed Merlin Milkbones. The only treats I use are greenies (not all the time as they're so expensive!) and mostly Old Mother Hubbard treats, which are all natural, with no additives or stuff like propylene glycol in them. However, I know other hounds who do fine on them. In this case, I guess I would err on the side of caution, take the MBs away, and see if he improves. He may have developed an allergy..?
Oh, and Wellness treats are great too, and don't have any gunk in them...