Pet urine can cause permanent damage to stone floors that have not been properly sealed. When urine is first deposited, it has a pH of about 5 or 6, which is acidic. It is much easier to remove when it is fresh. Once it dries it turns alkaline (pH of between 10 & 12) and becomes trickier to remove.
If you have a cleaning job that has proved too difficult to complete yourself, you may need to call in a specialist.
I came across a company called ‘PHS Cleaning & Restoration’. This is a company based in Illinois with many years of experience cleaning natural stone floors. They seem to have quite a comprehensive evaluation process, before they start any remedial work.
By the way, I found this great image from www.dailypuppy.com. Click on the image to see more photos of ‘Sophia’, the Golden Retriever.