What type of underlayment are we talking about? Is this 'real' plywood or is it OSB?

There are enzyme treatments out there (forgive me...I don't have the names handy...someone else will chime in and offer a name) that can be used to neutralize the odour.

Once the odour is neutralized, many people will seal the plywood/OSB with a primer like Zinsser. The two things combined usually do the trick.

Of course the way to get 100% removal of the stains is to remove the top layer of your subfloor floor and reinstall new plywood....but that's now what most people want to do.

What is your new flooring going to be?

Hi SJ - thanks for the insight! I believe it's real plywood. The new flooring will be a vinyl. Any chance you remembered that enzyme neutralizer?

Replace the subfloor.