This happened to me as well. I did not get a 100% duplicate. Closer to 95%. So it was a bit scary for me to delete the double tracks.
I had a problem that the double slashes in the file path was replaced with a single slash. It probably happened by a screwup with the Move and rename tool. All the stuff did not change paths because of the recent import job I had done. I also managed to rate all this tracks before I found that the rest of the tracks was duplicated. So I had 95% of library in wrong path with ratings and a lot of other tags, and 5% newly imported with updated tags as well.
In my case I turned off the auto import and saved the files of the newly imported 5% to a playlist. Then I deleted the files in the correct path (the duplicated 95% + the newly imported part of the library), because they had been auto imported again and was missing some values. I used ~d=a in the search field to make sure they was deleted for good, so the auto import would work again at a later time. I moved the base path of my music to a temp directory, and used the "File and Rename" tool to set the patch values straight, then moved the music back in the correct directory. I did this because the rename would not actually be done on any real directories, as a single slash in the Windows world is not well appreciated. I then turned on Auto Import and imported the new 5% of files. Everything was back to normal.
I think you can avoid most of this, but just remember to delete only the newly imported part of your library (to preserve play count etc), and use ~d=a and delete the correct tracks with the original paths if needed, to make sure the Auto Import add everything after the job is done.
