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If you used "Erase then copy" or "Smart Update", Petter, the files should definitely have been erased. Perhaps the Finder didn't update? Try restarting your machine and taking another look...
If that doesn't help, please send me a copy of the SuperDuper!.log (use the support email address), which you'll find off your Home folder in Library/Logs. I'll take a look and see if there's an explanation in there.
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--Dave Nanian
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