Right at the end of the episode Kovacs tells Rei that the only reason she wouldn't remember what happened in the shuttle was that she was restored from an earlier backup. Rei confirms this, and then goes on to tell him something Quell said in the shuttle immediately before the explosion.
Takeshi figures out that Rei can not remember what happened on the ship because she was backed up before the attack. Rei confirms this. Takeshi asks Rei how she could kill Quell. Rei responds by quoting what was said right before the ship exploded.