I don’t think this is at all possible. We have Jon Connington’s POVs. He thinks about both Septa Lemore and Elia at different points, and so surely we would know if they were the same person. It would be very weird if that never entered his head. Added to that, his thoughts about the two characters were different.
Most importantly though, I fail to see the point of keeping her identity secret after Aegon’s is revealed. Not only would her identity being revealed win Dorne over, it would prove Aegon’s identity beyond any reasonable doubt. I can see the reasoning for her not revealing her identity while Aegon hides his, but after that it’s pointless.