You're screwed (happened to me on my first patrol), but I was far away from any ports. You COULD submerge and use batteries at 1/3 speed, then surface and sit there a long time, and repeat. (Batteries recharge on their own even when stopped and surfaced, though very slowly).
Of course, depending on how far away you really are from a port, this may or may not be a viable option.
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Its not a bug... its a feature! 
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