How can i stop itunes from finding duplicate tracks from my external hard drive?

All my music is stored on C: drive and backed up on an external hard drive. when I install I iTunes it detects all tracks from both sources giving me 20000 duplicates.  I have tried uninstalling iTunes and then installing without the external drive plugged but iTunes still shows both copies, only the f: drive version has the ! next to it. How can I get iTunes to only search in one place?

Uninstalling and then reinstalling iTunes doesn't reset the library. To that simply delete the iTunes Library.itl file in the iTunes folder. For completeness delete the other files in that folder and the subfolder Album Artwork.
Don't let iTunes scan the computer, or if you do disconnect all of the additional sources of media. Better not to scan and then use File > Add Folder to Library so you are in control.
See Backup your iTunes for Windows library with SyncToy for a suggested method of keeping the original and backup of your library in sync.
tt2

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