I know this won't help your current problem but when we moved into our present house and had carpet put down, we paid extra to get a Pet Pad to go under the carpet. So, any pet mistakes do not penetrate the pad or subfloor underneath only the carpet.
Believe me, I have lots of sympathy for you in your situation and wish I had a great remedy. We had a cat who lived to be very old and had problems her whole life. I tried everything with limited success. That was years ago and I hope there is something more effective on the market now. Good Luck!