Saving submerged is fine in the stock game. What is more likely is the game restore always sets your map to a default zoom, but your marks and plots on the map might have been created with another zoom level. Try zooming in and out a bit and you might find your marks return. I frequently save just before getting into position to attack and have no problems with the save restore surfaced or submerged in the stock game. Also make sure you are patched to V1.4.
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