Well, the rotten floor and the smell, which I can imagine how unpleasant it can be, indicate that it absorbed water. Also, check for any leaks for the toilet, though I doubt it if you say you changed. Either way, you must cut the floor and the subfloor and change them completely. Otherwise, I don't think you can eliminate the odor. This happened at my grandma's house, but I let professionals do it. They changed the toilet and the floor entirely. We found the toilets at a reasonable price on
bathroom-supermarket.co.uk.