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Fauna is just one person, and people are much more likely to believe a group over an individual. Just like what happened with all of NijiEN forming a narrative against Zaion, if everyone says there's no problem with management and Fauna can't talk about the specific problems because of her NDA. Everyone will side with the remaining Hologirls over Fauna, and Cover will survive this rough patch just fine. Nothing can destroy them short of having a Selen type disaster in the future. Obviously they don't have to actually smear Fauna like what happened with Zaion, but convincing people that the management problems are happening to only Fauna should be a piece of cake and the fanbase will eat it up. Instead of seeing management as a company wide problem, people will just write it off as Fauna's personal issues with the company. Everyone will forget all about it soon after she graduates, and will get distracted by the next gen or a cool Holo event.