If the Jupiter's anything like the empeg car player in this respect, then the current song running order is stored on a specially-formatted "scratch" partition, separate from the rest of the software. It's not stored in a file.

The layout of this special partition is not completely known. It's proprietary, and the folks hacking on the empeg car player are only just beginning to figure it out.

The reason it was done this way on the car player was disk/shock/powerloss protection. A failure during this write operation to a regular hard disk partition would cause irritating things to happen, like long disk checks. By keeping their own format and keeping the partition separate, they can protect the data using their own more robust techniques.