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If the third wire isn't connected to anything, you've turned the three phase alternator into a single phase one. With no circuit on two of the coils there's no current flowing in them and they're not making power, so no problem. The risk is whilst clearly you're getting good AC voltage that the reg/rec is turning into ~14V DC, you're probably only getting 1/3 of the wattage(amps) out of the active coil, so over an extended period your battery isn't going to receive enough charge to keep it topped up. I wouldn't head off on any long trips until you have the right reg/rec.
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