Season one right after Clovis dies some servant comes to bother the emperor and he says he was just talking to Clovis, and the servant reacts with a huh? because he is already dead.
I.E the mental elevator can talk to the dead, even though this did not occur at all in the episode where they were actually in there.
So yeah, continuity fuck up. But, if it is supported in the final episodes by some event it will mean that the Emperor knew since then that Lelouche started the Black Knights and became Zero.