You have to de-activate
Auto-Import Background Scanning before you clear the Library, or it'll re-import everything pretty much right away. That's the most likely cause of your central problem. Auto-Import is still looking in your old locations on disk, and is re-importing the stuff there.
If you
really want to "nuke" it completely, do this:
0. Make a
Library Backup and save it somewhere in case you later decide this was a terrible idea.
1. Close MC.
2. In the Finder, use the Go menu and choose
Go to Folder.
3. Paste in:
~/Library/Application Support/J River4. Delete the
Media Center 20 folder.
5. Re-open Media Center and it'll be fresh and clean with nothing left over from your previous installation at all, except the License.
But, that's kind of a low-orbit ion cannon way to fix a problem. If you ask about what you need, we might be able to help you fix it without such a sledgehammer approach.
Don't worry about the Licensing. The way I listed shouldn't nuke your License, which is stored elsewhere. However, if it does, you can
restore it at any time (in fact, you're allowed to use a single License on any Macs you own, within reason).
By the way, if you haven't borked it all up yet, or can still go back to before you decided to move to the external disk (everything is still on your Local disk too), you can use the Rename, Move, and Copy Files tool to migrate everything from within MC without re-importing anything:
http://wiki.jriver.com/index.php/Rename,_Move,_and_Copy_Files