You can disable the shadowc by adding a file to the nkp11 folder on the E partition. It is ShadowC_off.bin or something like that. If you don't have an NKP11 folder (older softmod using nkpatcher10) you can add that file to the root of your E partition. ON the next reboot, you will see the real contents of your C partition.
I can't follow you considering the backups. You can simply ftp your xbox C and E partitions over to your pc and use them together with xboxhdm to create a bigger harddisk for the xbox.
regards.