It had such a stench of cat urine that even after the owner was out that we had to wear respirators to walk into the house.  

They chained their new pledges to the wall and urinated on them.

Blacklight plus vinegar should have done the trick for urine.

I don't know, but I'm guessing perhaps there was a leak/flood and the subfloor rotted, and/or pet urine that soaked into the subfloor, and/or mold issues? 

Where you can run into issues is pet urine.  

The hydrogen peroxide should remove any stains and eliminate the urine odor.

I use Urine Gone, but I'm told Natures Miracle does a good job too.

There is feces and urine all over the floors and you can imagine the smell. 

Unless there are holes, deep gouges or black stains from dog urine, I would sand and coat them with several coats of poly.

@Alexander Rodriguez so, the challenge is all you know about is the dog damage - there may be more:(Would NOT recommend letting them try to fix the floor damage - they will just make it worse, or may even hurt themselves and sue you.Pet urine is NOT easy to remediate.