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If moisture has stained the wood, how will lightly sanding the finish get rid of the stain in the wood itself? I don't see any way that the stain could be removed without bleaching with oxalic acid or sanding it out, and both of those will definitely affect the existing stain.
Your (OP's) situation is a tough one. Doing a spot fix and touching up to match is nearly impossible for someone without _lots_ of experience (read mistakes/failures). It's not clear from the original post whether this is a new house or just new to him. If you can contact the previous owner or builder and find out the manufacturer of the flooring you could buy some replacement boards. Cutting out the old stuff is the easy part - getting the new boards to fit tightly and stay in place is much tougher. Again, something where lots of experience is necessary.
An alternative might be to use a polyurethane with a darker stain in it. This is basically just a coverup, but a rather simple one to do. You'll have to screen or sand the whole floor to give the new finish something to bite into, but the odds of success are much greater.
R