Keep it in the format appropriate to the information. If just the text is important, Markdown is probably fine. If the structure is important, keep it in HTML.

Keep it in the format appropriate to the information. If just the text is important, Markdown is probably fine. If the structure is important, keep it in HTML. If the layout is important, PDF. You wouldn't store a Gutenberg bible in Markdown, would you? (Don't answer that - there's always one asshole who would)