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What brand and type of paint? If it is anti fouling paint then it is made for continuous immersion and will reduce/eliminate any marine growth on the hull. Yeah, bottom paint changes, fades, if it is an ablative paint ( the best to use for a trailered boat) but that won't hurt it. The older whalers all have water in the foam. some very little, some are very wet. Have you seen this boat in the water? Where are the motor well scuppers relative to the water? if they are above the water I wouldn't worry too much. If you moor or slip store the boat you have to repaint whenever the ablative paint wears off. I don't understand why he would put anti fouling paint on a boat that isn't stored in the water. Read the paint manufacturers website. Good luck. You'll love a Whaler.