Speculation.
@Tizoc:
Oh so she was killed off cuz the fanboys/fangirls of Geass can't accept Lelouch living happily ever after?
That's part of it, I think. Geass isn't pure escapism, the writer wants to tell a meaningful story, and a happy ending is almost always pure escapism. That's why, at best, we get something that's ambiguous. Bitter sweet endings are more common, like in Gurren-Lagann.
The main reason Shirley was axed was so the plot could focus on bigger things, since she would always be anchoring the show down. However, rather than just ignore her, the writer chose to give her a bigger role by having a meaningful influence on the plot.
@Crossword:
Maybe it's possible for a person to be Geassed by two different Geasses. That is, Lelouch erased her memories of him, and then the Emperor's Geass added on the whole ''Rollo is Lulu's true brother'' thing. Basically, you can't be Geassed twice by the same Geass, but there's no limit to the amount of Geasses that can be put on you, if that makes sense.
It's a retcon IMV. Lelouch's Geass was always portrayed as permanently rearranging the circuitry of the brain in such a way as to induce an action, so there shouldn't be a way for Charles to "add onto" Lelouch's Geass because the individual has already been affected. My idea is V.V. kissed Shirley, then Charles gave her a brand new Geass that incorporated what Lelouch did to her.
It would make sense I guess when Charles tries to Geass Shirley and it doesn't work, though this opens up the plot hole of how Charles could Geass Lelouch in that big scene in Turn 02. Maybe that was a fake memory too. D: