the easiest thing to do is go into your itunes program, and delete all your music *CAUTION.... Itunes will prompt you with an are you sure you want to delete... say yes... you'll then get a second screen that says remove files to recycle bin NOOOO you do not want to delete the actual files... you are just deleting the reference to the location of those files so Itunes knows where the music is...
After that... simply go to file/add folder to library, you will get a popup box, point it to your itunes music folder and it will be an accurate representation of what music you have.
In the future... delete music using itunes... and when you get the dialogue box that asks you tot send to trash... hit yet, and it will delete that reference, as well as the file itself... hope that helps.
Jason