Are you talking about the oil based primer kilz? If so are you thinking of painting the floor?

If so i dont agree with painting but thats neither here or there.

If the cat stain is contained locally to the wood planks then kilz will help and should dramatically help reduce the odor. If the stain has made its way to any subfloor then kilz wont do much.

If you are not intending to paint the floors then dont even bother with kilz.

Kilz original works great at this but it is white paint. How does this relate to refinishing hardwoods?

If it seeped into the hardwood, it's NOT refinishable. Or it is, if you enjoy the smell of pee on a warm summer morning. :( It gets into the boards on the sides and underside, all of which cannot be sanded out. It's replacement time. Kilz is for the subfloor or joists after you pull out the flooring and before you put down new flooring. If the subfloor wasn't too damaged by the pee too. Kilz is for the walls, and baseboards and any vertical surfaces that could be subject to the pee spray. That's if the surface is going to be painted. If it's going to be stained, you have the same issues as you have with the wood floors, and just hope the shellac coated it enough and there were no gaps between the woodwork and wall for the pee to dribble down into.

A house with cat pee is really a complete gut if it's bad.

"A house with cat pee is really a complete gut if it's bad."

Entirely agree and the same with dog pee also.

Unfortunately, I have had to deal with this before. The rental we moved into while we're building had this problem. It had carpet and vinyl flooring which we took out, so I was able to treat the sub floor. So your case is slightly different.
What I did was sprinkled baking soda on the floors and let set overnight, vacuum up, reapply, I did that for a couple weeks. ?? The worst areas I put a fairly thick layer, places that seemed ok and no odor I just gave a light dusting. I also bought some pet odor enzyme spray and sprayed the floors, so I would alternate spraying with enzyme spray and the baking soda. I also tried to keep the windows open as much as possible. When I finally thought I got it all I coated it with several goods coats of polyurethane. Then I put new flooring on top. It worked well for me. Just fyi- I also had to treat a couple walls, I wouldn't have thought about it, but there was cat odor there.

I would not be tearing stuff out until I knew for sure where the smell was coming from and you say that you are not sure.
Is it one room? Is it every room? Do you have friends with sensitive noses that might be able to tell if it is localized or general?

Try a black light.

Air the place well then try to sniff it down.

Natures Miracle is supposed to be good. When using enzymes, do not use anything else first. That can interfere with it's ability to work. Follow the instructions on the label. Shake first.

Remove and replace any exposed material you find. Kilz Original the rest of the subfloor anyway.