What Geass was Anya still afflicted by?
It was not officially said but it was implied that Charles had actually been using his Geass on Anya for years to erase her memories. If you remember Jeremiah activated his Geass Canceler right after Anya revealed that she had no memories. Presumably, the memory erasing was to prevent her from discovering Marianne's presence or some similar event. Throughout the series Charles is the only one was is able to erase or delete memories and he is also in a key position to be erasing them and he would want to keep Marianne existence hidden.