Yeah, definitely try not to save within 32 kilometers of any ships if you can help it (Try to do a quick soundsweep before saving), and I think within 50 kilometers of land. Saving while submerged is also a big no-no.\
Also, one tip I've heard is to overwrite your save: I.e., make a save called 'Patrol xx' and then make another save right after also called 'Patrol xx.' (Or I think that's how it should go) I don't know if that really has any effect, but since I started doing that, I haven't had a corrupted save. (Not that I had very many bad saves before that though
)
I know this doesn't really help with your current Lost Patrol, but maybe for future reference?