I may be the last one to have this problem but apparently Go Daddy changed my site to Cpanel. In doing that my content was duplicated on Cpanel server with a new user name and numerical IP. . My guess is to prevent errors the old server data was left in place. To upload new content you must log into your Godaddy account and get then new user name and numerical IP address to upload the new content to. You must change the user name and IP in your FTP client.
I am not sure what your question is but when the new hosting plan is ready to go live make sure the domain is pointed to the IP address for that plan, otherwise it could still be sending traffic to the old hosting which would eventually be shut off.