Missing files in music app

Apple Music

I was storing all of my Apple music files on an external hard drive. The hard drive started going bad and some album files were erased. I was able to transfer my files to a different hard drive but with the some of the missing files.

When I open the music app on my Mac, it still shows the albums that are missing tracks in my library, but if I go to play them  I am asked to locate them which I can’t because they are missing. 

Luckily I had a back up of the music library on another external drive that I use only for my Time Machine backups. I loaded the entire music folder with all of my files into the music app. 

The music app only loaded the albums that had the missing files. But now those albums show two copies of each song in the album. So when I go to erase either one of those extra tracks, the track that’s saved in the music folder is erased. Is there a way to fix this problem. I tried to consolidate the library but it doesn’t fix it.