I have never had any problems saving over existing games. What I have had problems with is when a patrol goes on for a long time. One patrol where I really noticed it was one where I started at Brisbane, sailed up to Guam to refuel and did four or five cycles of sailing out from Guam, using up my torpedoes on a convoy and then returning to Guam for refit. As the patrol went on it longer and longer to save and load the game and finally the saved games would not load at all.
Finally to rescue the campaign I went back to the last good save and then made a beeline back to Brisbane to finish the patrol. Once the patrol cache was flushed it worked normally again.
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