More information will help to identify the softmod like list of files on C drive.
How did you conclude some hdd space is missing?
But my own take is why bother? Just change the softmod to something with proper LBA48 support:
1. Backup eeprom with configmagic and transfer to PC for safekeeping.
2. Get Frosty's xbox rescue disc and Kingroach's ndure.
3. Cold-boot with Frosty's , gain ftp access , make backup of C drive contents, delete everything on C, copy in files from Kingroach's Ndure C folder. Make sure ernie.xtf goes in first before xbox.xtf in the xodash folder.
4. Also ftp in Kingroach ndure's E folder to E drive.
5. Reboot and you should have proper LBA48 support. Configurable options are assessible from E:\ndts\default.xbe for LBA48 (All to F , F/G under nkpatcher option).
6. You may need to reformat F/G drives with xbpartitioner.