It sounds like you’ve recently moved your files to a new location? If so, have you properly added this new location as a watched folder in your Roon settings? With that, did you remove the previous watched folder location? You mention you already cleaned up your library, which should update any old storage paths that no longer hold any media.
Can you explain the difference between your storage locations ‘MusicData’ and ‘MusicData2’? To confirm, you do not have your backup storage location located in the same folder as your local library?