We updated the import code so that the import is now done in the backend. This should greatly improve stability - we used to have problems with importing larger projects.
At the moment, importing does not delete the existing files - it places the imported files on top of whatever you have, so what you're seeing is the expected behavior. Some users have been confused in the past when they tried to import a project and their server.js disappeared, so we're trying something a little different.
You can create a new project containing only the files from a GitHub repo by going to https://gomix.com/#!/import/github/<GitHub user>/<GitHub repo>
That code hasn't yet been updated to use the new import, so you may have problems with larger repos until that happens.