I've never had save game problems in either SH3 or SH4 by following three basic rules: Save only when surfaced, never save when within sight of another vessel, and save only from the map screen.
I realize many people like to save just before a torpedo shot, and then reload if the results are not to their satisfaction, but that kind of play never held any appeal for me. Though of course, any game should allow the player to save anywhere and under any circumstances. Be thankful we don't have some craptastic console checkpoint system in place. Yet.
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