We will be fixing the floor first. If we go with the maple flooring it will be nailed to the plywood subfloor. That is how this flooring is meant to be used as it is tongue and groove flooring.If it were me, I would find the source of the wet/damp before painting and deciding next steps. It may have a simple explanation like your tenant having a cotton rug where he let his wet boots drip dry, but it might not, and the "might not" possibilities would worry me about smells. I think pulling the floor up to look is an excellent idea.
I would put a liner under your maple to let the floor move a bit relative to the new maple as they are probably going to be in different states of water content/dryness. Just my $0.02
All the best,
Peter
Eric