Read it, tried it, and it still does the same thing...I guess I'm just not bright enough for JRiver.
Moving the files "properly" will work best if you do it first. You can use, generally, the same process to fix already broken files, but this might be challenging in the state you have your Library in now. However, MC automatically makes backups of the Library, and saves them in your My Documents folder. So, what I'd recommend now that you've already moved them is as follows:
1. Find a copy of your Library Backup from before you made the move.
2. Turn off
Auto-Import background importing for now.
3.
Restore the Library Backup (you can pick only the Library, as you don't need the settings).
4. Now, since you've already moved all of your files, when it loads this Library, all of the files should be "broken". That's okay, as we can fix the broken links.
5. You can still use the Rename, Move, and Copy tool to "move" them, and since they're just broken links, it'll actually just move where MC looks on disk for the files. So, basically, you're going to use the Rename, Move, and Copy tool in "Update Library Only" mode, to "move" the files within MC from where they were before to where they are now.