Updated my itouch gen 4 32g to Ios 5 and now itunes can't find music files

I did a search and could not find anything about my specific issue.  I was hoping to get some help if possible.
So I did the update to IOS 5 and everything went fine..........except for one thing.  I have all my music stored on an external hard drive so I changed the media folder location to my external drive.  When I did the update IOS changed the location to "C:\users\name\music\itunes\itunes media folder".  I figured this is why itunes could not find the files.  So I switched it back to my external drive and it still could not find my music files.  The weird thing is that I can sync it and it won't delete the music from my ipod.  All of the music is still on the ipod but not on itunes.  I know I can manually go in and find all the folders but I REALLY don't want to have to do that.  I have done it before and it took 7 hours.  Since I don't use all the files I can't just drag the library over and problem solved.
One other strange thing that happened:  After I did the update I downloaded an app off of the the appstore in itunes.  This is the first app that I downloaded off of itunes and not straight off my ipod.  I then recieved an email from apple saying it had been downloaded on a computer or device not associated with my apple id (which makes no sense seeing how the id on my ipod is the same as on itunes).
If anyone has a suggestion on how to fix the music problem, I am all ears.  Thanks.

Once a track is in your iTunes library, you should not touch it except through iTunes. But I guess you know that now.
iTunes, to answer your question, cannot "refresh." If you re-add those files to your library, iTunes is unable to match them with the existing library entries, and will create a bunch of duplicate entries. This is a longstanding shortcoming of iTunes (and the source of lots of traffic on this fourm).
If there are "too many to manually" reassociate, then starting over, in the sense of deleting and then re-adding, may be a good plan.

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