Shirley seemed to treat Kallen being in the knights as new information too once she got de-geassed, which makes no sense either because the whole council obviously remembers that they found out she was one of them during the Black Rebellion.
It's best to write both off as LOL SUNRISE, or if you want to think about it more a 'bug' in the way Charlie's Geass works. Lelouch not recognizing her in a bunny suit as Kallen but still remembering Kallen as being someone who was in the student council but then left after being outed as a member of the Black Knights could have been simply because he has more memories of her as a member of the Black Knights than as a fellow council member, so when he was wiped of his memories of being Zero it messed with his memories of her such that he remembered her but did not recognize her- an inconsistency born of the fact that 60-80% of his memories of her were suppressed. If Kallen were to have said upon meeting him 'hey, it's me, Kallen from Ashford, remember?' he might have gone 'wait, why the fuck didn't I recognize you?' and some messy things might have ensued, especially since Rolo was present.
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It's best to write both off as LOL SUNRISE, or if you want to think about it more a 'bug' in the way Charlie's Geass works. Lelouch not recognizing her in a bunny suit as Kallen but still remembering Kallen as being someone who was in the student council but then left after being outed as a member of the Black Knights could have been simply because he has more memories of her as a member of the Black Knights than as a fellow council member, so when he was wiped of his memories of being Zero it messed with his memories of her such that he remembered her but did not recognize her- an inconsistency born of the fact that 60-80% of his memories of her were suppressed. If Kallen were to have said upon meeting him 'hey, it's me, Kallen from Ashford, remember?' he might have gone 'wait, why the fuck didn't I recognize you?' and some messy things might have ensued, especially since Rolo was present.
(whoa that last line sounds kinda suggestive)