Quote Originally Posted by Kraco
An interesting and highly important detail is, of course, that the emperor didn't rewrite Lelouch's memories. He just suppressed his real memories and implanted false memories. This was made evident when our favorite witch returned Lelouch to normal. He could once again access his old memories but still the false/new ones as well.

Now, manipulating someone's memories in such a manner is indeed quite a powerful and sophisticated technique so I wouldn't put it past the emperor to be able to reset Lelouch's constantly on geass as well.
The implantation did rewrite/temporarilly some parts for him having his geass deactivated and for him not being able to access memories from when he was Zero and CC and so on.

This may be just little details and it may be a bit boring to discuss such, unless this proves useful in future eps, like the contact lens.