hmm, you finished Kahlil's route in 1.4.2, right? Now that you've replaced the persistent, the game will now think like 1.4.2, that you've just finished Kahlil's route. But if you finished Kahlil's route in version 1.3, then it's 1.3 persistent data that you need to copy and paste.
I hope you're following me >_<
if you start a new game and you can skip through the prologue, then it works! Other things you can check is if you go to the gallery and see Kahlil's CGs you've unlocked that means you did it correct
Edit: if not, maybe you can copy everything inside your old 'saves' folder and paste it to the newest one?
Oh and another thing you can try is type %AppData% in your folder address go to RenPy folder and in Bermuda folder there, you will find another persistent data that you can change