Cissnei was last seen in Crisis Core boarding a Shinra helicopter with Tseng giving her orders to locate Zack and Cloud before the Shinra army does and bring them back alive. She was last heard talking to Reno and Rude about their mission's status over the radio and asking the pair to search for the targets at point 120.
As those who have played through the original Final Fantasy VII game would know, this mission ended in failure for the Turks. However, as opposed to Tseng, Reno and Rude, who also make appearances in the original game and the movie sequel to FFVII, Final Fantasy VII: Advent Children, Cissnei simply disappeared and was never heard or spoken of again.
If we take a look at the final few episodes of Before Crisis that took place after Zack was killed in Crisis Core, after the Turks tried to “save the world” by defeating Fuhito, the scientist of the first iteration of AVALANCHE, and Zirconiade, the “World Burner” Fuhito summoned to destroy everyone on the Planet, the Turks members that were involved in this fight were all knocked out before Zirconiade was killed, with the except of Tseng, Reno and Rude, who were involved in another mission to save the captured Veld, the former leader of the Turks.
Due to the Tseng's decision to help his former boss, who defected Shinra to save his daughter (who was the leader of AVALANCHE) during the last quarter of Before Crisis, the Shinra Executives wanted the Turks to be disbanded, while Scarlet and President Shinra wanted the Turks to be killed for insubordination, even with Tseng, Reno and Rude as the only three remaining (known) survivors of the whole ordeal. It was not until Rufus convinced President Shinra to let the Turks continues its operation that Tseng, Reno and Rude (and later Elena) lived to become the meddling antangonists they were in the original game.
In the epilogue of Before Crisis, which took place during Meteorfall (after Sephiroth used the Black Materia in the original game to cast Meteor), while the Turks were evacuating the civilians of Midgar, Veld, as well as the Turks' old colleagues, arrived in Midgar to help with the evacuation, hinting that they were not actually dead after the events of Before Crisis, but rather went into hiding instead, since they were thought to be dead.
Since Cissnei is one of the eleven playable characters in Before Crisis, it can be assumed that she was involved in the fight with Fuhito and Zirconiade, and it is quite possible that she was one of the Turks members that went into hiding after the events of Before Crisis.