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I finally got the re-install to work.
I un-installed Calibre. I cleaned every entry referencing Calibre from the registry (quite a few). I found a Calibre folder at c:\Users\<myusername>\appdata\Roaming\Calibre and deleted it.
This time when I re-installed I accepted the default location for the library in My Documents and was presented with an empty library. I then re-added all my books and all was well.
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