While reading this thread and loading my savegame last evening I ran into the same issue !!! I heard about it a few times now but still hoped that it would never happen to me...
I tried to load an earlier savegame but the result was the same: diving to some 500m, accelerating to 128 kts and an LI who tells me that we are way to deep - but hey, still alive...
The only savegame of this patrol which loads coerrectly is one where I was forced to leave the game very quickly due to some family buiseness.
I saved while I was just about to attack a merchant at close range. Now I want to try to figure out if I can make it home with just pausing the game or simply by ending the patrol and wasting me left eels...