I can't give you a specific answer without any details. What are the temperatures in the enclosure? What substrate are you using? What do you normally feed the gecko?
Too low temperatures could be a cause for the pneumonia, but you would see other signs other than lack of appetite.
Liver disease is something that the vet would need to treat.
Was the vet a qualified reptile vet? It doesn't sound like it, as pneumonia and liver disease are completely different illnesses and would have differing symptoms. A qualified reptile vet would have been able to give you a closer diagnosis.