Thanks for the fast response
Doesn't solve my problem but I will try Sigil.
I try to sum up my problem in a sentence or two: What could be the reason that Calibre converts the epub in a way that there are no line-breaks anymore in the mobi? Is there some css-command in the epub or so that I could try to add to solve the problem?
I doubt that two-column-pdf-export would work with the pdfs I want to convert because they have really complex layouts. Not only two colums but text-boxes that are spread throughout the PDF, sometimes text on top or on the side of the pages that aren't needed in the epub.
An example would be the
Eclipse Phase core rulebook (CC-licensed). I just need the "background"- and not the rule-sections of the book but even copy+paste is kind of a pain in the a**