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The converted output files are written to the same folder in the calibre library as the input ones.
Most of the time you do not need to know where Calibre has stored the files. If you want to export files out of the Calibre library you can use the Calibre 'save to disk' feature which allows you to specify the location (and formats) you want the ebooks to be saved to.
You can also get calibre to send books to your eReader device using it's Send to Device feature. Again there is no need to worry about the location in the Calibre library used to store any particular file.
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