Technically, what I think happens (if SH3 zones work in similar manner to SH5 zones), is that in heavy seas certain damage zone types that are designed to flood/get damaged when at specified depth are repeatedly being submerged below their "trigger" depth for a moment because ship is rolling on the waves so much, resulting in more and more flooding over time. If the ship leaves rendering area before flooding damages it too much, it will survive, but if you keep contact with it, damage is increasing faster than its crew repair rate and weather doesn't change, it will eventually sink.
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