Weird duplicates situation in iTunes

So a few hundred of my songs have duplicates. When I check the info, I find that the duplicates are "located" in other folders in my music folder. When I click "show in Windows Explorer" for the duplicate song, the correct folder opens (i.e. the folder in which the song is supposed to be) but the file is not highlighted (which it is if I do the same with the "proper" song.)
For example, I have two instances of Aaliyah - Try Again. In the summary tab for the proper instance, next to "Where" it has the correct file path "D:\Music\Pitchfork\Try Again.mp3". When I look at the same for the duplicate, the file path is "D:\Music\Break - Shaolin Soul\..\Pitchfork\Try Again.mp3".
I moved the "Break - Shaolin Soul" folder to my desktop and checked to see if I could still play the duplicate track. I could. (All the duplicates are playable.)
This is utterly perplexing, and I would greatly appreciate any help.

I don't know - it may depend on how you choose to add files to your library. There will be more than one path you can choose using the iTunes Add folder to library option or when "dragging & dropping" onto the iTunes window. If you use a different path from the one used previously then you will get duplicates. Using one of the following tools could help make sure you use a consistent path.
*Adding new items/removing orphans*
Try iTunes Folder Watch or iTunes Library Updater. Folder Watch is much faster on the adding files front, can be set to run in the background and includes a useful exclusion feature, however it’s really slow at removing orphans. iTLU is better for this although doing it manually after looking at a list of proposed removals generated by Folder Watch is probably faster still. iTLU can also be set to update iTunes when you've used 3rd party tools to change tag info.
If I recall iTLU also has an option (syncroclean) to remove tracks that are not in it's watch folders, which might provide a way to detect & remove the duplicates though it's not a feature I ever tested.
tt2

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