vacuum pump will help, but I dont think I would go buy a pump just for that small repair. I would use a drill to remove as much core as I could through the hole, then fill it with epoxy.

I assume boat is stored for the winter up off Lake Erie. If there's water in the core, it'll be a lot softer come spring due to freeze damage! I agree with both Flexpat and Shine, the vacuum will work but it will take time; if you heated the deck AND could pull the vacuum on the core down below the boiling point, the water would theoretically flash to vapor immediately. However, even if you can't reach the flash point pressure/temperature conditions, water will still evaporate, only it will just take longer. You could probably figure out how long it would take to evaporate all the water but it would be a complex calculation involving dew points, relative humidity and psychometric tables, etc.!

If boat is laid up for the winter, time is the one thing you have plenty of! If boat is under cover or shrink wrapped so rain/snow can't get to the deck, I would drill some holes in the soft area and soak it with denatured alcohol. That should prevent freeze damage, and help dry it out as the alcohol will combine with the water and then remove it as it evaporates. But if boat is shrink wrapped, make sure it's well ventilated! If it's well sealed nothing will evaporate! If you repeat the soak/dry cycle several times over the winter, it should be fairly dry come spring, when you could soak it with Git Rot, which is very thin and penetrates rotted wood real well.

OK Guys. Thanks. I am shrink wrapped and have along cold winter ahead. I'll try to use the holes that the rail mounts to the deck with as breather holes. I'll do the alcohol/ heat lamp first and see how that goes.

Git Rot - I've heard of it but never used it. Is it an epoxy based material ? Does it fill all the voids and solidify ?

Located on Long Island - The boats in the Lake Erie area must turn into literal ice cubes each season. Cold up there !

Yes it's a very thin epoxy; the idea is that rotted but dried wood will soak it up by capillary action, and it will then solidify. Kit comes with a squeeze bottle with a separate bottle of hardener. I don't think standard kit is more than about 6-8 oz., so might be worth calculating how much volume you need first. You can probably buy a low viscosity epoxy from other suppliers such as Jamestown Distributors or our own Shine for less.