To me there were signs of Lyse while she was pretending to be Yda. Even though Krile (I think?) jokes about Lyse getting her Archon mark in punching we can probably safely assume that was what Yda got her marks for as a thesis on the merit of pugilistic fighting techniques. Thus to me Yda at least knew how to write a good enough paper/report for Sharlyean scholars to turn their noses up on. Where to me Lyse even while pretending to be Yda had many an instance of being the ditzy blonde. Also, maybe their eye color was different thus part of the reason why she refused to take off her mask or get a new one. They focus on her eye when her mask gets split during the Bloody Banquet escape. In the pre EW story focused on Fordola Yda doesn't come off as a ditzy blonde.