Happened to me, too, sank a ship in shallow water; continued the patrol and then at least a day later, running submerged ran into the wreck and severely damaged my boat. I'm not sure how long sunken ships "exist" for, but there is a radius around a sunken target which makes it disappear if you move outside it. I'll have a look at some of the files and see if it is controllable, or - as I suspect - hard-coded.
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