The files exist in your hosting plan, correct? Someone might have an easier solution than the following but until someone provides something easier, the following should work.
First do a backup. You can download the entire web site to your local system.
Then (within the host) move the files in the root (the domain files) to a separate new directory (except there are a few you do not want to move), then move the subdomain files to the root. Then move the files in the new directory to the empty subdomain directory then delete the empty new directory. You might need to get help from GoDaddy to decide what files to leave alone in the root directory.
Note that that procedure would not be good for a production site that must be continuously available and reliable.
Alternatively, you can create a new version of the web site locally in your system then wipe out the existing web site and then upload the new site. I do not know how much it costs to get GoDaddy to take a backup of your system but if you want to ensure your web site is protected you can get as many backups as possible first before doing anything.