You are correct, upload all file option will automatically replace all your old files with the new ones.
It is very much recommended to do this once you get a new product release.
However, If you still see any issue or in a doubt, can anytime contact your host and ask them to delete the old files on the server, and then you can reupload your current site.
Thanks for that answer.
I use a small WS_FTP LE program to upload and download sites from another server and I can't use it with the Muse files so I was looking for a download option and yes I can ask the host to zap them if required.
Oh ok, the download option at present is only available to Business Catalyst hosted site.
So yes, the best option will be getting all the files on the server cleared and reupload the site.