If only
"Some" of the old floor boards that are water damaged, why not replace only those ? OR if they are only discoloured, use them as your subfloor to the Plasteak.
This sounds like an excellent idea and should last for the life of the boat.
First step is to ensure the original boards are absolutely dry. If they are a sodden mess, don't do it, go for new solid plywood. It's a real carpentry job to do the seams properly starting with new plywood. I've been looking at renewing my floors with new teak and holly plywood for the last few years as they only have 10 coats of varnish, cured in a hot box, and indent very easily as the teak and holly plywood are as soft as balsa. I didn't know about epoxy and how to apply it clear using glass cloth back when I got the boat new 26 years ago. This is the surface after removing all the boards and polishing them AGAIN last spring :
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They look good from afar but far from good.
Remember, you will be hermetically sealing your subfloor and any remaining water in there will have nowhere to go in hot weather. This will generate enough vapour pressure to lift large areas of epoxy and give you a floating floor.
Read this epoxy manual below for the proper application of epoxy. I think this written material applies to most epoxies and the epoxy doesn't have to be System Three (ST) although I have found ST to be about the cheapest and lasts the life of the boat. I did my companionway stairs with one layer of glass cloth and about five coats of ST plus two coats of varnish, many years ago. The rough strip on each step is embedded crushed quartz for non slip.
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Prepare your boards well and remove any loose varnish. Finish with #120 paper front, back, up, down, port, starboard, north, south, and side to side. Thin your first coat of epoxy well (as found in the manual) with lacquer thinner. Everything must be 100% sealed or suffer the consequences. Once the epoxy is fully cured, any glue used for the Plasteak should stick