To my limited understanding… it will take the elements version mark down files and overwrite your work you did online inside the dashboard…
My markdown files were in the CMS folder on the server - get your final modified versions and perhaps load them into elements as needed…
Then you can do republish all files 
Just an FYI
Went in to server - downloaded CMS folder
Loaded Md files into elements
Republished all files…
No issues - works great 
I figured this would happen so I deleted all my markdown files in Elements, so none get published.
My new workflow is I write all my articles using One MarkDown and then just paste it into the CMS Online editor. So I have a copy on my hard drive, but not in Elements. Also, with Elements web hosting there is a backup on the server in case I ever need to recover.