There is another possibilities why Kohana is not influenced by Dark Falz Elder, but subjected to Code: Abyss issued by the Six Council.
Look at this way, Kohana is a veteran Arks which is said to be candidate for Six Council. The kicker? Fourth is missing at the moment. What Genesis Weapon Zeno use when he is promoted? Gunslash, which Kohana is used at the moment.
It might be possible that Kohana might be well aware to what is sealed within Naberius, and she is silenced due to knowing too much. Long time players should know that Rojio, a researcher, gets himself into a hitlist due to poking his nose too much into Naberius.
At Episode 2, Maria did stated that No. 2, 4 and 6 member are the counter to the Three Heroes unchallenged power. To maintain the power, Either Luther or Regius himself already tried to get rid of any potential threat. When Luther found out Kohana is going to escort Ash's party (instead with other Arks which has more seniority), he use it as a chance to issue Code Abyss to her to try and remove Ash and Afin and grab Matoi. Failure to do so, forcing her to flee and get herself assassinated by Quna.