Well, I always update the Sandbox whenever I update Macintosh HD. It ensures I'm working from the same base, and converts any "new" applications to shared ones.
"Cloning back" is certainly safe if you have a backup, and I do use this fairly often to apply an "approved" set of changes to the base. It's easier than reinstalling everything, but they are -- in the end -- basically equivalent.
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--Dave Nanian
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