[Zubersoft]

Song versioning will change nothing in regards to how files are managed and stored. The easiest way to fix this is to first switch "Create Subdirectory per Song" back on, then create a library backup file under Settings->Backup and Restore->Backup Library, then restore that backup under Settings->Backup and Restore->Restore Library from Backup. This will clear out the storage location, then extract all the files and place them in subdirectories.

Mike