Recently my apt flooded, and it is a basement apt with a concrete floor under the carpet. The professional flood expert came out to help me get all the water out, and I learned a little about concrete floors. He taught me that concrete is actually quite porous, and absorbs moisture well, that is why it is used for foundations. It absorbs excess moisture and wicks it to underneath the house into the earth. I was concerned because I felt that we didn't get as much water up with the vac than what had flooded, even though the walls, carpet and pad were dry. He said that it had already been absorbed by the foundation, and only time and gravity would wick it down the rest of the way. He said that it would wick down faster than it would have time to mold or mildew.
Anyway, I am just sharing this to show how the cat pee could be trapped in the concrete. The moisture from the pee could be gone, but the hormones or whatever that makes the pee stink smell so bad could be trapped under the surface.(this is just my guess) I am so sorry you have to go through this, cat pee is the worst. I personally would call a flooring/cleaning expert at this point to get some tips/advice. Good Luck!