The entire contents of the entire game are on each disc. The only exception are the FMVs. They can't all fit on one disc so they're spread out among three. When you reach the end of one collection of FMVs you have to switch to the next one.
That said, it's conceivable that certain errors might lead to going to a place where you shouldn't be. The data is still there for that location, and the FMVs only get referenced by an index of file names. Since the game says "play FMV 9" it'll play whatever the 9th FMV is and not care the content of it.
From my reversing of it I can say that it only checks the disc number at four points. When you start a new game, when you load a saved game, when it's time for a disc change, and (in the case of the PC version) when you run the executable. The new game only ever checks for the first disc (obviously), the next two will look for a disc defined in the save-game data and the last one (for the PC) only wants to know if there is a disc.
So no where in the field script does it care, or even have access to, what disc is in the drive. As long as it passes through those three/four checkpoints the game will continue to play.
During a disc change, the field script just sets the next progress value for you to continue on from where you were once it passes the "next disc please" prompt.
EDIT:
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