My big question about Charlotte is why send an Archaeologist? Obviously she has some idea of "what" the Island is, maybe involving past civilizations or cultures. I can't imagine they would send an archaeologist to look into the past 20 years, has to be something more.
As for how she knows, well how did Daniel know how to fix the computer? And why was he worried that he wouldn't be able to do it? Is this part of the card thing they were doing on the beach? Obviously they have inside information on all things Island, the big mystery is where that info came from.
Sorry for adding more unanswered questions!