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What I got from the scene where Keido and Segai were watching Haruka take the case and run is that Haruka most likely had the third genome with her from the very beginning (or the anime, at least) and kept it hidden from Keido and GHQ. That's why Neo Gai had to forcefully take Shu's.
Of course, this theory still has some questions that need to be answered to work but to me it makes the situation more believable until they either disprove it or give their own explanation.
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