Nestor's technique is fine unless the wood has been compromised (beginning to soften and rot) from the excessive moisture. Since you've already painted this with a latex, it's a wait and see proposition. If the coating begins to come up, it means that the wood was compromised.
In this case, after scrapping off anything that's coming up and not firmly adhered to the wood surface, a liquid epoxy wood hardener will strengthen the compromised areas. Just let it sink in and dry, then repaint again. We use this stuff all the time. Our favorite is by Abatron and can be found in most paints stores.
If you have an uneven surface from chipping paint and such, a hi-build primer like Mad Dog or Peel Bond can help even out the surfaces for a smoother looking finish. You can ask the paint store if they have any small samples of Mad Dog. I know my paint store has been giving them away. It's probably enough to do a window sill
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