I'm so sorry about your lil guy.
I had a lil fella' that wasn't gaining weight, and after 2 weeks we found out that he had heart failure. He lived for 9 weeks, but was born with the defect. One of the ventricles to his heart was narrowed (we had an ultrasound and necropsy done), so the blood wasn't pumping to his heart correctly. Because of this he wasn't thriving/gaining weight. He ate very little. When he went into heart failure, we were given the choice to treat him symptomatically until he eventually passed (very poor prognosis), or have him put to sleep. We chose to put him to sleep. It was one of the worst days of my life. I hope your little guy beats the odds and proves everyone wrong! We will be praying for him.
Great to hear the other pups and Mom are doing well!!! xxxxx