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Thanks, I was unaware of that App Nap feature. Before I read your reply I had completed several other SuperDuper runs and the problem had never resurfaced. Nonetheless, I turned off App Nap for the program as you suggested.
Even with the impaired display in that earlier run, the log indicated that the run had completed properly and when I repeated the SuperDuper run with smart update, it copied no additional files, indicating that the clone was in fact a good clone.
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