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Sparky -
Lets say you initially installed calibre portable to
Y:/Calibre Portable, and you moved your libraries into that folder and all is well
When you install a new version of calibre portable it will pop a folder location dialogue - browse to
Y:/Calibre Portable - and select that folder, viz: where my D:_Sandpit folder is the equivalent of the root of your USB drive.
It that doesn't help, could you take a screen shot of the root and other directories on your portable drive as it is now and post here. Best way to post images is to go into Advanced mode and click the paper clip icon.
BR