The same thing happened to my little guy in July. He had coccida and was being treated for it and then developed a second parasite. He was 11 weeks and only weighed 1.1. He was real sick but after his hospital stay I never left him and feed him every 3 hours. He too won't eat so I hand feed him for 2 months. Now he is a healthy 2.1lb little boy. Now my vet says he is too full and to feed him only 3 times a day with hard food out all the time. That has been working well for him. I use two foods both soft and hard. Wellness and Innova because he is sooooo picky. When all else fails he will eat his wellness puppy cookies. He might be a tad spoiled
Hope your baby feels better soon. I know its hard now but with the proper care you'll little one will be running around enjoying puppyhood before you know it.