How would you handle this?...

[Ed E]

If the contaminated area is limited (and as Shorty suggested, you can determine this by moisture sensors and black light) then you can treat small areas by injecting bio-enzymes. These products consume the odor causing bacteria, and are very effective, in my experience. Having said that, I bought a porty to take care of two issues that I felt must be attended to by HWE. Pet contamination is one of those issues.

I turned down a job two weeks ago where the pet contamination was so severe, my only recommendation to the homeowner was pull the carpet and pad, check the subfloor, and replace the carpet and pad.