Go to the Windows button, All Programs, QlikView, QlikView Enterprise Management Console, and your browser will open showing the Server Management Console. Now browse to System, Setup, QlikView Server, click to expand, click to select your QVS and on the right part go to the tab Folders. Set there the new "Root folder" after having removed all document licenses and tasks for the QVW applications, if any.
Then copy or move all files from the old folder to the new one.
Hope that helps.