I’ve got a document which I originally wrote in Markdown, and copied into a scrivener document as plain text.
I converted all my headings to scrivener styles (Heading 1, Heading 2, Heading 3) but left the character formatting (like bold and italics) as is. Everything worked great until I tried to compile an ebook.
I created a new compiling format based of the generic ebook, and set up my styles and selections without a hitch. The project compiles fine - the styles show up formatted the way I want and the sections are laid out as I desire – until I check the “Convert Markdown to rich text in notes and text” box.
Once this is checked compiling the project yields odd results. Specifically, it strips the return from after any of my heading styles, moving the paragraph which follows up into the heading line and applying a style to match. The next paragraph returns to the correct style, and all is well until the next heading is encountered.
As soon as I uncheck the markdown conversion box everything returns to normal.
I’d be happy to share my project if it would help.