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You can stick with the bat file if you prefer, there's no difference. If you want to switch to using the exe, download calibre-portable.zip, unzip it, and then copy the contents of CalibreConfig to "Calibre Settings" and CalibreLibrary to "Calibre Libray" and it should just work. Keep your old folders around until your sure the new ones work.
The only difference with the new calibre portable is that it is truly portable, in that it does not require the installation of the C runtime from Micorosoft on the host computer.
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