I wrote a tool that does this, somewhat. As written, it starts with a folder of markdown files, converts those files to HTML, then turns the HTML to ENML, and creates a .enex file, which can then be imported into evernote, preserving file modification dates and formatting, etc. It doesn't currently support embedded media however.
In your case, since you already have HTML, you could add a feature to this tool to start at the HTML stage; pull requests welcomed...
https://github.com/karloskalcium/md2enex