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Without your backup volume connected, look in the folder named Volumes on your normal starup volume for a directory with the same name as your usual backup volume. You can check that it is it the one taking up lots of space by using Finder's Get Info or du -sh <dirname> at a Terminal command line.
Delete it (be sure to empty the trash if you use Finder; or very carefully use rm -rf from a Terminal command line).
The problem is that when the backup volume suddenly disappears (i.e. you unplug it while SuperDuper! is working), the ongoing file copies end up being stored on the boot volume.
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