This is outside the scope of my project. I do not use PHP.
However, I wouldn't save the HTML. Rather, keep the human input markup text saved. How you save it would depend on how PHP handles things. One option is to simply save it to a database and retranslate it to HTML with a server side Markdown to HTML translator for PHP. To keep things fast, you might consider keeping both the Markdown input and the translated HTML. Then only update the HTML when needed.
Mike