After hard drive replacement, iTunes points to wrong drive

I have my iTunes media on an external drive, and the drive failed. Luckily I had a backup, and I also had a spare drive to replace the bad one with. So I set up the replacement drive on my Mac Mini, naming it the same as the old drive (iTunes Library). I then copied the data from the backup onto the replacement drive. I then connected the replacement drive to the Mac, and started up iTunes. From the looks of everything, it looked like all was good, all of my Music, Movies, etc. was there. So yesterday I happen to look at the path for one of my Music files, and I see that now iTunes is pointing to my iTunes Backup drive, named "iTunes Backup", instead of my regular iTunes drive, named "iTunes Library".
I had thought that iTunes would still know that the replacement drive, named the same as the old one, would still point to it, but apparently I was wrong. I even went to "Preferences" and pointed the Media location to the replacement drive, not the backup.
So, my question is: How can I get iTunes to point to the right drive? Do I have to open iTunes with the "Option" key and have it point to the replacement drive? Is there something else?
At least I had a backup, and both replacement and backup drives seem ok...
HELP!!

Well, it is complicated in the way your public library does things is complicated.  iTunes keeps a catalog of media files and assumes from that catalog that the file exists where it was noted to exist when it was added to the library.  Just as with my public library, there can be off-site storage too, but they have to make sure somebody hasn't moved their books without telling them or they are in a mess.  As I said earlier, I have no idea how your catalog on the internal drive got into its head to use the files on the backup drive.  That goes completely contrary to how iTunes has ever operated from all the topics I have seen on this site for 10+ years, unless there was something else you did that I am not hearing. No matter, if this is truly the scenario.  What I am having you do is deliberately break all the links to the files on the backup drive and hopefully rebuild links to the files on the new library drive.  Then you will be using the other document to change the location of the rest of your non-media library files so it is all together on the library drive for easier moving in future.  I guess you could do it in either order.  The thing is, the library file (iTunes library.itl which ties all iTunes together) is telling you (according to what you report) that when you request track XYZ in iTunes it should be going to the backup drive and play file xyz, but you want it to go to the library drive and use the file there.  If you simply copy the library file to your library drive it will still be trying to find the music file on the backup drive.  The only ways to change the designation are to either breaks the links and take advantage of iTunes' re-linking tool, or to use the editable .xml version of the library file to hand-edit the file paths and use that file to rebuild the library file with come concurrent loss of data that is only in the .itl version.
What are the iTunes library files? - http://support.apple.com/kb/HT1660
More on iTunes library files and what they do - http://en.wikipedia.org/wiki/ITunes#Media_management
What are all those iTunes files? - http://www.macworld.com/article/139974/2009/04/itunes_files.html
Where are my iTunes files located? - http://support.apple.com/kb/ht1391

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