I agree with Peejay and Dave,
I would be best to remove all the old finish back to wood. Make sure it is completely, dry then coat with resin and cloth, I am just familiar with epoxy. I would not use polyester.
Trev

Chance are the water has impregnated far more than you can see. From my experience with models of a similar age and provenance and as others have said you need to remove all the paint back to the original wood to see exactly where the damage has occurred. You need to replace any hull part that is no longer sound and as Peejay says cover the whole hull with a fine layer of thin glass cloth and fix with either layup resin or similar (Eze Kote from DeLuxe materials) to provide a watertight hull. You can then rub to a smooth finish and apply primer and top coat. Modern paints are much different from the enamel paints and easily available from most suppliers.
dave976

If you are concerned about watertight integrity, you may wish to put a layer of thin glass cloth over the hull. The point of glassing is to prevent the wood structure from separating when it gets wet.

I lost an old Scientific Models Nautilus submarine because it cracked from the inside, and there was nothing on the outside to prevent cracking and distortion.

Agree wth Nerys. If you clean up the hull and paint it will then be one color. Rick

From what you say, I'd be inclined to rub pack and paint the whole of the hull. If you try and patch there could well be differences in the paint.

Nerys