No, don't delete this file: it'll just get recreted by the system.
The problem you're hitting is an intermittent thing we've seen on some Tiger systems. Since the file itself is recreated by the system, and is disk dependent, it's OK to ignore. I've attached a script you can use to do so (the script assumes you're using "Backup - all files") -- just download and unzip this to the Library/Application Support/SuperDuper!/Copy Scripts folder, and then select it in the 3rd pop-up ("using script named") in the main interface.
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--Dave Nanian
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