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If you do the conversion via the Calibre GUI then the converted books are always put into the same folder as the source book. To get such books out of Calibre you need to use the Save to Disk option after converting.
If you use the Calibre Command Line interface then you explicitly control where files are placed, but you have to know how to work at the command line level so this is nowhere near as convenient as using the Calibre GUI.
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