I don't pay any attention to what I'm doing when I save. I've even saved with a torpedo halfway to a target and no problem. All that clear sensors, on the surface, outside of sight of land, smooth seas, while burning incense and facing Mecca stuff is from SH3 and doesn't apply to SH4.
But corrupted saves do happen. I always save just before I enter port and again just after I leave. And I might save after a significant event. But I'm convinced that what you are doing when saving the game has nothing whatever to do with the corrupted saves. They just randomly happen and we make patterns where there are none: basic human psychology.
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