It is possible to empty CDFS partition with is sometimes annoying.
You can take out HDD from caddy and connect to desktop or plug by standard usb/sata adapter. Partition will not be recognized. Wipe hdd for few sconds and put it back to the original caddy. With buffalo secure lock manager (HD-PXTU2) regenerate partition. You will have blank hard drive partition and empty virtual CD partition.
I can't find any solution yet to edit this virtual CDFS partition, but for other models and brands solutions you can find here:
http://blog.usboffice.kr/?p=146