These are just ideas I'm tossing out there. I'm not saying I even think this is the problem, but something is causing this to happen. Does your vet have an ultrasound machine? If so, he could check for stones and such with it. Good luck.
I did find this:
http://www.executec.com/urolith.htm
And this:
Kidney problems in Yorkies
Q: Is it normal for a breeder to write on a dogs papers "not to be breed"? We got him when he was 4.5, and told he is the large type and shouldn't be breed. Our Yorkie is only 8 and has kidney disease. He is showing symptoms and the vet said he has a few weeks to go. Is this a genetic trait in Yorkshire Terriors? We may get another one but want to know if this is common in this breed of dog. Regards Stephen
A: Stephen- We have seen more purebred dogs with contracts that specify that the dog may not be bred recently than we did in the past. I think this is becoming a fairly common thing.
I am not aware of familial or genetic tendency towards renal disease in Yorkies but that doesn't rule out the possibility. They do get bladder stones pretty readily, based on the ones I see in my practice.
Michael Richards, DVM
http://www.vetinfo4dogs.com/dkidney.html