What is the url to your site? Secondly, to which directory did you ftp all the new site files?
Your files should be uploaded to the “yourdomain.tld”, as set in the Control Panel Domains–>Manage Domains–>Edit screen for the domain in question, directory and not the “home” directory (which contains Maildir and logs.
If you accidently deleted the “yourdomain.tld” directory when you “purged” everything from your “home” directory, you can just add it again via your ftp program’s “create a directory” command, or by connecting to the shell via ssh and using the mkdir command (mkdir yourdomain.tld - executed in you “home” directory).
Once you now have a “yourdomain.tld” directory in your home directory along with Maildir and logs, re-upload your files into that directory (or “move” them in the shell) and you should be good to go.