Sera seems to have known Conan was Shinichi before they first met recently. Masumi remembers Shinichi from some meeting they had in the past and has been since trying to encourage Conan to remember where he met her. In "Conan vs. Heiji, Deduction Battle Between the Detectives of the East and West" episode, it's confirmed that Sera knows when she thinks "Now we already know who's the winner" while looking towards Conan that thinking about the case, referring him as "Shinichi".