If I am understanding the problem correctly, you'll need to manually change the <FolderBase> of each TV show and <automaticFolderRoot> for each movie. It sounds hard, but it is easy.
Exit TVRename. Load up C:\Users\<username>\AppData\Roaming\TVRename\TVRename\2.1\TVRenameSettings.xml with your favorite text editor. <username> being your username. Before you start, make a backup of TVRenameSetting.xml and save it away in case you make a mistake with your editing. Then use the Find/Replace function of your text editor to change the old folder to the new, preferably using Repeat All. Do this for both <FolderBase> and <automaticFolderRoot> and then save the TVRenameSettings.xml. Restart TVRename and your library should show as being in the correct location.