I've just checked it again and I'm now SURE that (in my instance of game) only the torpedo load is 'forgotten' by game, bu the upgrades, medals, crew changes and all this stuff remains intact after reloading game, and still being in base. So I always give medals and so on after returning from the patrol, then I reload the game with SH3 Commander, fix torpedoes and sail away. Never had any upgrade lost nor any other change forgotten (like lacking crew etc.).
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