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Calibre never recognises my Calibre location on a update. Every time I install one, I have to remember to click Advanced and change the directory to where my last install was installed. It always tries to put Calibre in 'c:\program files\calibre\' (if I'm remembering the path right), while my actual install is under C:\users\<myname>\calibre\, and always has been. If I forget to change the path on the update, I get a copy of Calibre with an empty library linked from my desktop. Maybe this is what you did? I just remove the c:\program files version and do it over with the correct path. Then my libraries show up again.
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