Joe:
I've never, ever seen it do anything like that before. What's even stranger, if you use "Smart Update" to do that, by definition it's going to try to *remove* things outside the selected set of files (Smart Update makes the destination identical to the selections from the source, removing any files or folder that are outside the selector -- as it says, it's just like Erase, then copy, but faster).
If you've got the SuperDuper!.log from this weird copy, I'd be very interested. Could you please send it into support so I can analyze it?
Thanks.
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--Dave Nanian
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