SD! will not back up to the internal if it can't find the external: there are situations where if the external fails during the copy we'll end up copying to a directory in /Volumes. He can use Finder's "Go To Folder" command to look.
But -- 6GB isn't necessarily an unreasonable amount of difference, especially if he hasn't restarted his Mac for a while... VM Swap files, sleep images, temporary files, spotlight index -- all can be quite large.
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--Dave Nanian
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