I have always been very leary of savegames with SH3... there are a lot of known and unknown issues associacted with saving games (saving too close to port, saving too close to other ships, wind/weather issue, saving while submerged) there are just too many little gotchas to make saving a game during a successful patrol worth it IMHO.
All of that said... i have NEVER experienced the crash dive of doom bug associated with saves, I have in fact, never had any adverse actions occur after saving or loading a game so i will be of little help here to you other than to say... if it can at all be avoided- never save... just finish out the patrol if possible is always the better option.
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