How about using the "Rename, Copy, & Move Files" function in the Library Tools menu. You can "lasso" all your files (or hold Ctrl key while clicking on each one) and then move them. I do this all the time for those TV Shows recorded on a different HD to move them to my TV Shows RAID drive/location.
EDIT: I reread your question and want to be sure that you are only moving the video, audio, images - (the "media") and not the MC settings too. The settings (like Themes, Views, etc.) are not stored with the library media files. But do a complete backup first - just in case.