Some things to try/examine in no particular order, and with no particular reasons or expectations
- If you have an ORIGINAL_EPUB file then remove or move it, and try conversion again
- Unpack the EPUB using Tweak Book ('T' shortcut) and look in the toc.ncx file - are there 50 or 59 entries ?
- Remove the EPUB file before the conversion
- Add one of the books that's giving you problems under a different title and try conversion
Have you tried the Writer2EPUB extension for Open Office - it maybe called Writer2HTML for Libre Office - then you may not have to convert in Calibre. MB member
theducks uses the plugin.
BR