When you upgrade your Free site to Premier membership, you do need to update your free site to Premier and upload it via FTP to your webspace again.
Please re-download the premier website from the members area, and re-upload it to your webspace. If you are unsure of how to re-upload please check the video tutorials in the members area for more info.
Please delete the old files of the free site and re-upload the premier website to a fresh install to avoid any problems. Unfortunately, the content will have to be copied and pasted back to the Premier website again.