No, the problem is that the "new" versions of the files were encountered before the "old" versions. As such, the new versions were copied and - since the hard link is "known" - tracked. But we never got to the point where we could hard link the "old' version to the "new" one.
An erase-then-copy will clear things up, after which you can go back to Smart Update.
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--Dave Nanian
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