As i see it, my options are these:
1. Reimagine the series with a daughter instead of a son right from the beginning, no transformations involved.
2. Write it as several unrelated stories, each one taking place as an episode/arc in the series, where a transformation happens as an event in the series. Some series might be crossdressing/TV/realistic TG, others might be magic/sci-fi.
3. Write it as a "shared universe" where all the stories take place, and the characters of different series know/meet each other, and for some reason sons are turning into daughters (either realistic or magical/SF)
4. Write it from the POV of the public/TV execs: Suddenly reruns of old series become... different. Somehow, the tapes of these old series were altered -- seamlessly -- so the sons are now daughters. It's a big mystery: doing it as CGI would cost hundreds of millions and take years of work, so it's far more than a prank. But what is it? Magic? Aliens?
5. Write it as a period piece: the *actors* that plays those sons suddenly and unexplainedly get transformed into girls. How is fifties/sixties society going to handle it? Will the TV execs try covering it up by recasting the roles or just cancelling the series? They might if it's just one or two, but if every damn series on air is affected...