Ubuntu – How to remove duplicate tracks from Rhythmbox

You can get around the one folder restriction by using symbolic links.
Say your music folder is ~/Music and you want to import ~/OtherMusic, you can put a symbolic link for ~/OtherMusic inside the ~/Music folder.

In a terminal: ln -s ~/OtherMusic ~/Music

You might need to restart your music player for it to notice the sym-link.

I had a similar problem with Rhythmbox. I don't have nearly the number of files you have, but it was not seeing new files or changed files. I did the following:

1. In Preferences --> Music, I unchecked "Watch my Library for new files".
2. Completely closed Rhythmbox (important).
3. Renamed the rhythmbox database - ~/.local/share/rhythmbox/rhythmdb.xml
4. Started up Rhythmbox and checked "Watch my Library for new files".
5. It started checking my collection and found everything.

It seems that my problem was an issue with the configuration file. I had reinstalled Rhythmbox, but had not done a complete uninstall. This left a corrupted configuration file in my Rhythmbox sub-directory. You may want to try this if it's possible that you have a corrupted configuration file.