Never save while submerged or within 50km of land or any object: aircraft or ships. H-J is correct; sunken ships can respawn if you save right after sinking them. Again, save at least 50km from your last sinking. It can be inconvenient sometimes but this is the only workaround that I know of.
Not sure if you know this already but don't use the Surface Attack or Surface Cruise buttons in the Crew Management screen. Using these buttons probably will result in a ctd. No solution to this bug except to move your people around manually.
Hope this helps...
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