Thought processes have inertia, just like in the diary, where she initially thought the Cultivation Room was unconscious, Bologue was also misled by Furya's appearance, combined with her demeanor and self-description, leading him to believe she was a trapped intern.
The truth was far from that.
Xilin's invasion caused the collapse and fragmentation of the Cultivation Room, and the completely isolated part evolved into the Ruins District, no longer governed by the Cultivation Room's will. Seizing the opportunity, she uploaded herself to the Ruins District, becoming its will.
Bologue doubted whether one person's consciousness could truly control such a complex and vast Void Realm. This might be the reason why the Ruins District continues to evolve towards chaos; even though Furya uploaded herself, she had no power to control the Ruins District, just like Bologue suffering from curse backlash, aware of his actions but unable to stop them.
