Zero was eliminated when each part of HiFuMi became possessed by her one at a time. They were pretty explicit about that part. The three of them were "closer" to Zero than Motoko's surface personality, so they would ease into it by having the three of them overwhelm Zero first. Kannami decided they should accomplish that by having each of them bring her out when they were in control. He was wrong in thinking that Motoko was a "host" personality.

Hibiki had her first, then Fujiko in the Okinawa arc, and finally Mikiri with the old lady's ohagi.

They weren't afraid of Zero coming out after that because HiFuMi "controlled" her in a sense. They absorbed her as a whole.