Have found multiple iTunes Library.xml files. Moved Library to new Hard Drive and it needs to be completely rebuilt?

Hello. I have a Mac Mini operating Mac OS X 10.7.2. I recently had to move my iTunes Library to a new hard drive. I followed the directions on how to move the library and refind everything yet when I do so what comes up is a mere skeleton of what I had. I have had to hunt down my purchased Apps, Music and Movies and re-add them to the library. I also noticed in doing this I have multiple iTunes Library.xml files ... shouldn't there only be one?  If so how do I clean this up without doing any accidental damage (i.e. how do I find the one that is being used and delete the rest?)?  If I delete the others is there any risk of losing purchased content? Lastly syncing my iPads has become a nightmare as I get the "This iPad is currently synced to another iTunes library" message. Obviously something

It's hard for me to picture the exact situation. It sounds like you still have your library file on the internal but some files on the external, and maybe some on the internal, some of which are in the library and others not...  By re-adding things after consolidating it may have made things into a hodge-podge. Yes, that article you referenced says: "iTunes for Mac: Moving your iTunes Media folder"with Media Folder being the emphasis.  You probably should have just moved your whole iTunes folder.  Still, moving the media folder as instructed should not have messed up the library.  Did you make the mistake of starting up iTunes before the external drive had mounted fully and it then told you it couldn't find many files?  How you proceed to sort it out will depend upon how much time you want to spend and how important things such as ratings and playcount are to you.  I have not actually used the consolidate feature across different drives myself (and don't feel inclined to do so here to test ).
If you are in the USA you can download some previous purhcases with iCloud, but not all.
Here's a bit on what an iTunes folder should look like:
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]
Library files with graphic and explanation of different iTunes versions - http://discussions.apple.com/message.jspa?messageID=13169517
Once you get iTunes working off the external drive it should just put new media to the external when you add it.
I have almost no experience with synching (I synched my neice's iPod, once, about 4 years ago).

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