If you want your subfloor cleaned, vacuumed and washed before new carpet gets installed then you will have to remove the old carpet yourself before your installation date and clean the subfloor to your satisfaction. If you choose to wash your subfloor, then it would need to be completely dry before new carpet can be installed. Strictly speaking, washing your subfloor is not needed for new carpet installation and is rarely done!
Now, getting rid of pet urine stains and odors in your subfloor before carpet is necessary and should be addressed before the carpet installation date. While we don't officially recommend any type of sealer/primer, we've heard good things about Kilz Restoration Primer/Sealer. It is supposed to seal off the stains and odors from pet urine in your base floor and could be the solution to that problem. There is never a guarantee that once you treat your subfloor with some kind of primer/sealer that you will never smell the odors in the future. At least not from your flooring company. Any guarantee like that would have to come from the manufacturer of the primer/sealer itself. Probably the only guaranteed solution would be to replace that section of subfloor but that can really be cost prohibitive so most people will just use the primer/sealer and that seems to work just fine in most cases in my experience.
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