That is awkward place to be. I would probably attack this in a series of steps. Assuming you are layed up for the winter, start by removing the floorboards to a heated dry location and give them time to dry out. The color MIGHT go away. If it does, then take the time to seal the sides and backsides, hopefully encapsulating them and preventing or at least slowing the water ingress.
If, after drying, the floorboards are still blotchy, the decision tree kicks in. Is it solid teak or veneer? Solid material can withstand stripping and aggressive sanding. Veneers, (plywood, lumber-core) are much more delicate.
Is the stain is too offensive to leave alone? If you are not bothered by it, seal the backs and sides and be done with it. If the stain bugs you excessively, use a paste or liquid stripper to get rid of the poly. Follow the directions for use and neutralizing. A cleaning with Oxalic acid or TSP should even out the color. Rinse with water to get rid of Then sand to smooth your work surface. If you have veneer be VERY careful not to sand through. If the stain is light, rather than the cleaning step consider a marine filler stain to even out the color. Regardless your choice if you strip the board(s) your goal is a smooth workpiece that is uniform in color, either from Sanding or bleaching/cleaning.
So... in the event you end up stripping the old finish off, regardless whether you clean and sand, or lightly sand and stain consider this fact: Cetol is a micro-porous finishing product. It seals out liquid water nicely, but it is in a sense porous to water vapor. This is a key advantage over varnish; inevitably even a perfectly-sealed piece of wood will be compromised, a dent, a ding, or a scratch is all it takes. You get liquid water coming into the damaged wood. It gets soaked up and turns into vapor. It can only get out through the same damaged spot though, which is a tough trick. A similarly dinged piece of wood finished with Cetol will allow the water vapor to come right through. It also touches up easily with no need for stripping. These two points make it a great product for traffic areas.
This is the place where I say your boat your choice, but if I were in your shoes and ended up going down the strip-and-refinish path I certainly would prefer to use Cetol on the floorboards over ANY other material even if my topsides and deck brightwork was show-quality varnish; it really is an excellent product for that application.
Regardless your choice of finish, coat your repaired floorboard(s) all-over, top, bottom and sides when you go to refinish. 4 coats minimum.
That's my $.02 on the topic! Holler if you have any questions further