Are you using two separate site definitions with the same local root folder, or are these two completely separate sites?
GS-01: Defining a new site | Adobe TV
Normally, that message will appear after a successful test of server connectivity, when you have a missing or incorrect root folder defined for the remote server. It also happens a lot with GoDaddy, they seem to be pretty bad at losing your permissions.
If you could post a screenshot of your remote server settings and a shot of your expanded Files window showing both the local and remote files while connected to the server, it could help rule out any site definition errors that may not be obvious to you.