I'm pretty sure that using the electric engines doesn't save fuel because they have to be charged with the diesel engines anyway. Thus, using the electrics and then charging them on the surface uses more fuel than only using the diesels on the surface.
That said, one can certainly use the electric engines to get back to base after the diesel has run out, if one is close enough. If not, there used to be a cheat, whereby the batteries would be automatically recharged if out of fuel... something about surfacing and ordering the charge. I don't know for sure because I've never used it.
One thing to keep in mind is that the faster the electric engines are run, the faster the batteries will drain. On the surface, there is one ideal engine setting for optimal fuel consumption for normal cruising and another, much higher, setting for travelling while charging. This is because the single engine used for propulsion while charging needs to work harder to bring the boat up to its ideal speed.
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