I once moved into a house and a family with 4 small boys had moved out of it. The bathroom was carpetted and the carpet and underlay around the loo had rotted somewhat, as had the floorboards underneath. Someone recommended I use Jeyes fluid (but it is quite toxic stuff I know!) I went back to the bare boards for weeks and just kept wiping the floorboards with the solution and letting it dry...eventually the smell of this permeated the floorboards.
My friend who visited me regularly got used to me asking her for a 2nd opinion on whether it still smelled awful. When we both thought it had I recovered the floor but not with carpet.
p.s Jeyes fluid is very toxic to cats and probably kids, I had a cat at the time and he was kept locked out of the bathroom during this process.