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This has nothing to do with rockbox, the gigabeat s isn't even supported. You should ask in the anythingbutipod forums.
You don't need to do any of this. When I replaced my drive I just formatted it as FAT32, copied the GBSYSTEM and .rockbox folders on to it from my old drive, put it into my gigabeat and away you go.
All I did when I received my drive was plug it in, create a single FAT32 partition, format it, and copy back the GBSYSTEM folder I had backed up from the previous drive.
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