Yeah, so turns out Kallen was freaking out back in the cave because she thought that Lelouch might have geassed her into being a complete Zero fangirl. >_> (Damnit entire cast, stop blaming your own character faults and whatnot on Lelouch! >_<)
The memory gap from 3 was so inane to her she hadn't even realized Lelouch used it on her already even after a whole year to think about it.
(unless she hadn't realized from the cave he couldn't use it more than once. >_>) But of course, Lelouch being Lelouch, who's
always valued his subordinates free will, he quickly put that fear of hers to rest.