One of the features I like about Scrivener is how the structure is transferred to RTF as bookmarks.
Is it possible that the bookmarks has some sort of MMD markup like “#” for level one folders, “##” for level two, etc…? Then Scrivener would translate, say, “# Title” to a level-one folder with the title “Title.” This would simplify reimporting stuff back to scrivener and keep using scrivener for a longer while in the writing process…