Second opinion is definitely warranted, and that by an internal medicine specialist.
And that to get a confirmation of an official diagnosis.
Having said that, and once you have the diagnosis, alternative remedies might prove more effective in the long run for a chronic non surgical condition that proves resistant to traditional Western medicine. How-ever the link below does talk about corrective surgery for cystitis polypoid.
problem.
Polypoid Cystitis in Dogs | eHow
Please let us know how you and your dog are doing, and seriously consider getting a second opinion from a specialist.