[Shohreh]

Thanks for the infos.

Suggestion: If it's the user who added the bookmark into the PDF, it's reliable, and Calibre could make it an option to use that info to find chapters.

Anyway, an alternative, simpler solution than adding+removing bookmarks is to… 1) open the PDF in a reader eg. SumatraPDF, 2) make a list of pages/slices that make up chapters, 3) use it to split the source PDF into sub-PDFs (eg. cpdf; one chapter = one PDF) 4) run Calibre to convert them into EPUBs, and 5) finally join them into a single EPUB.

It does nothing to help converting PDFs into clean EPUBs, but at least, Calibre will know where each chapter starts and ends.