Your fear is warranted. Smart Update makes the destination exactly resemble the selections from the source, so your restore will end up with *only* your Home folder on it.
The secondary problem is that we won't let you copy to the boot device.
Doing a similar thing, with "Backup - all files", and then booting from the backup & restoring should work, though... unless the sync done by Server keeps some sort of "state" file on the laptop.
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--Dave Nanian
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