Considering the second part of the problem I'm not sure how It even works after a republish ..pretty sure you are not placing the files in correct folder (or they would dissapear after publish instead of appearing)
What folder are you using to upload?
If your answer contains the platform folder, I can tell you already that it should't.
As for the mime type problem some configurations done at the application level are lost on publish because the web.config is regenerated.
Set the mimetype at an higher level, like web site or web server.
Or create a separate virtual directory to have the files served (solves your other problem) and set it there.