One of the bedrooms in our home has smelled of cat urine since we bought it. Since then our cat has sprayed in there once about a year ago, and pooped in there two months ago. We decided to replace the smelly carpet with wood floors after the pooping incident. We just removed the carpet and the foam, and the room still smells. Does anyone know of a way to get rid of that seemingly permanent smell?
it's probably too late since you already put the floor over the old one. try spraying some vinegar and water in the area. That's the only thing I can think of. don't use oils or sprays they are toxic to pets.
I would also recommend you to try the baking and vinegar solution or the dish washing detergent with the vinegar solution to remove the smell.. I have the Custom Area Rugs installed in my living room.. I used it for this rug.. It worked for me..

I had a cat that had kittens in one bedroom

unknown to me the kittens had deficated along the border of the carpet in the room. I made a paste of baking soda and vinegar after removing the deposits I took a scrubbing brush and scrubbed each spot with the paste rinsed with clean water & sponge and then covered the spots with just dry baking soda and let sit overnight until dried the vacuumed the soda up and you couldn’t even tell a cat had ever been in the room let alone pottied everywhere

worked for me only thing I know of I didn’t put soap in my paste it worked . I suppose the soap would work also just harder to get the soap up??? Vinegar/Baking soda my go to for Odor removal