I have had it happen to me several times, but with only minor damage.
I did lose one boat after saving a few weeks ago though. Loaded my save, and got reports of massive damage/flooding. Clicked external cam to find that I was beached. Still have that save, and still don't know how I managed to travel 2nm off my original path to end up on a beach.
FYI: I was going through the Lombok strait when I saved.