I've got input.
Strict vegans live an average of 17.9 years longer than people who eat meat. At least, according to the statistics I'm aware of. Now we can play "who's got better statistics" all day, it won't prove either case. I find that people who are unfamiliar with a vegan diet really aren't qualified to say that it is harmful.
If it were my son, I'd have a nice consult with Brenda Davis, a registered dietician who is also vegan. She can probably explain what's happening to your son.
If you can't reach Brenda, let me know and I'll give you another recommendation. Brenda can be reached at firstname.lastname@example.org
Also, protein in the urine... I was told by my obstetrician when I was pregnant that first morning urine should not have protein, but after you've been eating, protein is always found in the urine. Just something I remember them telling me; I don't know if it pertains to your son.