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If you have your library at Y:\Calibre Portable, you should install the next version at Y: Calibre will warn you that there's a previous calibre installation and will ask you if you want to update it. Say yes and all you your settings will be maintained. You won't lose your libraries and you can't set them at any directory you like (it is not necessary them to be inside the Calibre Portable directory).
In this way, calibre won't forget your libraries. There's a problem, however. If the drive letter changes from a computer to other, calibre won't find them as the path are fixed, not related to the directory itself..
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