Had the game a few days, I've had both saves (first patrol each) disappear from the game
SH3 is pretty finicky when it comes to saving. Some people have problems, others not so much, but here are the general rules to follow when saving:
Save when surfaced only
Don't save until 50k from port
Don't save near convoys
So basically just try to be clear of everything and anything, while surfaced, b4 you save, just to be on the safe side.
Basically you're saying unless I do a full patrol I run the risk of losing my saves? This is a pretty awful bug.