First, I'm very sorry about Junior.
I'm really not sure where the vet is getting his/her information, but it sounds very wrong.
Dogs who have surgery for liver shunt can live long and happy lives.
They probably will need a special diet and supplements, but that doesn't mean that they aren't happy...
If done at a good place, there is about an 85% success rate and 95% survival rate. Junior may not have as good of a chance if he is very small, but I wouldn't say he doesn't have a chance at all, esp. if he hasn't seen a very highly specialized vet (and maybe even two).
Liver shunt does not damage the stomach; however, is can cause diarrhea and vomiting because toxins build up and the liver doesn't filter them properly. Liver shunt does cause bladder stones and infections which in turn can cause bloody urine. If stones are present, they can be removed.
And the hospital stay is 2-3 days. It should not be anywhere near two weeks.
How old is he and how much does he weigh?
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