The only substance I know of that works fairly well for reducing odorous compounds is hydrogen peroxide. The only thing I can think of is try ‘soaking’ or washing the sub-floor with a warm or hot water/hydrogen peroxide mixture. Maybe try a small area and see if it makes a difference. Let it dry and see. Normally, I would think that removing the sub-floor might be the option.. just suggesting other things to try. You might also find a black light useful because it will allow you to locate where the urine has affected the wood.
