I believe what you had to do was:
1) Beat the game on one file
2) After watching the ending, when the game asks you to save, SAVE ON A DIFFERENT SLOT
3) Then, go back to your first save (before you fight the final boss) and you now SHOULD be able to do 2nd playthrough bonuses on that file now
However, I'm not sure if this was carried over to the 3DS version. I have it myself but didn't finish a playthrough yet on it.