I believe that it will
My thinking:-
1. Since the same game is used to re-make the eboot, the save games all go to the same place, normally each PS1 game (official) would have its own 2 memory cards of space
2. Most games that have 2 or more discs will ask you to save before switching, just incase something goes wrong loading the second/third/forth disc, save the game, exit that disc and load the next one, hopefully the save game created by the last disc should be acessable
This is my hope atleast, back to FF9 :thumbup: