Fe7, I assume?
If so, did you also change recruitment?
I've noticed that the characters who are in Lyn mode will often show up with the portraits of those in their recruitment slots until Lyn mode is complete. And, when you start from or continue into Eliwood/Hector mode, those characters will still think they're the genders of their recruitment slot, rather than whoever they became.
Also, anyone know if recruitment slot, character, or class decides who's levels count towards the Ilia/Sacae route in Fe6 and the snow chapters in fe7? (IE, if Shin is an armor knight and was recruited where Gonzales should be, does leveling him lead me towards Sacae or should I level whoever appeared in his spot? Or maybe even just level nomads?)
EDIT: And also my save file just stopped working after I suspended the game. For whatever reason, the rom overwrote the save with totally blank data. Any clue what caused this? Its happened before so I have a backup of a few chapters back but I'd really like to know for the future >__>