Como encontrei em este link , método 1:
1) Convert with calibre to HTMLZ.
2) Replace the .htmlz extension of the file with .zip
3) Unzip the file
4) Create the PDF with Adobe Acrobat Pro using "Create from webpage"
Método 2:
If you are looking for a fast solution and don't mind sacrificing the internal links, simply open the Calibre-produced PDF in Mac OS Preview, go to the Print dialog, and from there "Save as PDF". This will produce a PDF that is searchable, with copyable content, but which lacks the internal links.
Existem mais soluções em este link , mas eu mesmo não as decifro.