Hey T-Top. Assuming you are using internal hard drives? With rekordbox closed, I would:
COPY everything from your old hard drive to your new hard drive, keeping the same folder structure.
Then on your old hard drive, move all of your music to a new folder so that rekordbox can no longer find it
Then open rekordbox and use the relocate missing files utility and all of your music should show up as being missing.
WITHOUT selecting any file in the list of missing files, click relocate and then navigate to the first file rekordbox asks for on your NEW hard drive (avoid using the search function so you don't accidentally select the same file on your old hard drive). Once you show rekordbox where the first file is, it will ask if you want to use the location of that file to relocate all of the other missing files. Click yes - I've found rekordbox is pretty good at doing this.
Once you are sure that rekordbox has relocated all of the missing files and everything's working properly, you can delete your music off your old hard drive.
If you are using two external drives, you can just copy everything from your old drive to the new drive (retaining folder structure), disconnect the old drive, rename the new drive to the same name as your old drive (including drive letter if you're working in Windows) and then when you open rekordbox it shouldn't be able to tell the difference! You can always use the relocate feature if it has any problems.
BriChi has even made a video of the process of relocating multiple files, see his reply to the OP... http://forums.pioneerdj.com/entries/25136231-Find-missing-tracks-automatically-