New iTunes folder on external drive...move xml file there?

About a year ago, I created a new folder on an external hard drive and I thought that I followed the apple designated steps to move my itunes music to that folder.  I then selected the advanced tab in preferences in iTunes and selected the new folder on my external drive as my "iTunes" folder.  iTunes seems to have worked OK for this past year using the folder on the external drive.  After updating to the latest version of iTunes (11.1.1), I tried to sync some apps to my iPhone 4, and I got the message that the external drive folder I am using as my "iTunes" folder on the external drive is not the one associated with my iPhone.  iTunes asks if I want to erase my iPhone and use the contents of my external drive folder on my phone.  This is the first time I have seen this message, even though it has been a year, and I have connected my phone to iTunes during that time.
In investigating this, I see that the .xml and .its files are not in the folder on the external hard drive.  In fact, there is no folder at all called "iTunes" on my external drive. They are still in the "iTunes" folder in my music folder on my internal hard drive.  This is what is still in the music folder in my home folder on my internal drive:
Should I manually move the .xml, the .ita and the other files into the folder on the external drive?
Thanks

In my message above, I tried to include a .png file of what my internal hard drive has in the music folder, but that did not work, so I am trying to paste it in here.  I am wondering if I should manually copy these files to the music folder on my external hard drive.  There is no folder on my external drive names "iTunes".

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