If by "3/4 through a second" convoy you mean you were in the midst of a convoy attack when you saved the game, then it's possible your save won't load because it was made when there were too many other units in close proximity to your boat and too much was going on to be successfully saved and recreated without data being corrupted or some other problem cropping up. Saving and reloading in a situation like that requires the game to remember and recreate a LOT of stuff at a moment in (game) time that already requires a great deal from your system resources just to play through it.
Corrupted and/or unusable savegames are a known bug with SH3 that has never been resolved; there are no guarantees, but generally the best way to avoid them is to save only when surfaced and out of range of land and/or any other units (ships, planes, etc.).
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