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Is the PDF file a DRM-free eBook? If so, that's a puzzling bug. But Calibre and the underlying open-source tool-chain it depends on for some conversions lack support for converting DRMd files -- which may explain your problem.
If so, use google to discover how to remove the DRM from the file. And remember to consider both the legality and ethical correctness of doing so. At a minimum, do not pass on purchased eBooks to others who have not paid for them, as neither authors nor publishers receive compensation when you do so.
Xenophon
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