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Why Kyuubi might have his Yin?
Take Juubi for example. He has his Yin and Yang, and he has his body (the mazou). Without any of the Yin and Yang, the mazou can still live and be use to create the zetsu. Thus, actually, Yin is the spiritual energy of a biju while Yang is his physical energy. Given that these two can be replenish with time and experience, I am incline to think Kyuubi already got his Yin back by feeding on Naruto and by also experiencing.