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It turns out that permissions to access Documents, Mail, Desktop and a few other folders were somehow "turned off". When I rebooted after the backup was complete, my desktop items were gone, as that folder in my home directory couldn't be accessed. My custom desktop picture was replaced by El Capitan. When I looked at the folder in the Finder, it had the small red icon on it, and I couldn't open it.
I finally accessed my home directory, and proceeded to "Apply to enclosed items" -- upon rebooting again, all was OK (although my desktop items were not in original locations).
I know that SD didn't cause this, but curious how it all occurred. I plan to run another backup overnight and check the results. Thanks!
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