From the image it looks like you previously stored your physical files in the MusicBee Library folder, which actually isn't a great idea. Keep your audio files somewhere in their own folder, outside of the MusicBee folder structure. MusicBee doesn't care where they are. The "library" it makes from them is just a file with data in it about what and where they are.
At this point instead of worrying about how to delete old libraries I would suggest just uninstalling MusicBee and starting over from scratch, this time with the Portable version. You'll have to re-do your past settings but it does a body good from time to time. But before you do that, first collect all your music files somewhere, then, BACK UP all those files to another drive or safe place. When you do the new install, do NOT turn on "auto-organize files". You can do that later, IF you want to (me? NAH!), after you fully familiarize yourself with what that actually will do.