Converting EPUB to PDF using Pandoc
Have you tried the latest version of Pandoc, which currently is v2.5?
Have you tried to play with '--epub-chapter-level=...'
numbers?
Have you tried to play with '--top-level-division=section'
(or ...=part
or ...=chapter
) for the output?
Have you tried with the LuaLaTeX engine`?
pandoc \ -f epub \ -t latex \ -o my.pdf \ --epub-chapter-level=1 \ --pdf-engine=lualatex \ test.epub
Have you tried a non-Pandoc tool like Calibre?