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rerunning the builder means what exactly?
It means connecting the player with a serial cable, and double-clicking on the file with the name builder_bigdisk.upgrade, as described in the drive upgrade guide.
This will launch the upgrader and install the builder image onto the player. When the player reboots, it will wipe any connected hard disks completely, repartition and reformat them, and prepare them for a new operating system and player firmware.
After that, you'll need to run car2_v2.01_hijack.upgrade to get a fresh copy of the player firmware on there.