Hmm, yes it's a bit like custom CSS then because it's altering the rendering even though the Markdown stays the same. The only way in this case is to restart the app.
But ideally there should be some kind of tag in the Markdown content that tells what citation file to use. Then whenever that tag is changed, the Markdown is changed, and the view update. That's the proper way in general because that way the Markdown text is self-contained - it has all the information needed to be rendered to HTML.
Can you think of any way to implement it that way?