Why does itunes convert my files.....again?

When iTunes scans my music folder (which is not the iTunes folder) it will convert some files and place them in the iTunes music folder. Because I don't want duplicates I took the converted files and moved them to my music folder, replacing the originals with the converted files.
When iTunes rescans my music folder it converts these same files.......again! and puts the converted files into the iTunes folder again making duplicates.
Why does it do that, how can I stop it, and why would it think it needs to convert a file that IS the conversion in made in the first place?

It's not automated. Because I add my music in bulk I initiate the scan by click on File > Add Folder to Library, and then just repoint to my music folder so it will add all of the new files at once.
Thanks.

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