Comentário oficial
If you are exporting to that same USB drive as your export device, yes, it will duplicate the files and occupy additional space.
It looks like you may have a bit of a mess on your hands, so I'm going to ask you to file an inquiry ticket here and our rekordbox support team will be able to gather some additional information to assist you in resolving this issue.

rekordbox is Replicating MP3 files inside the external hard drive is this correct? (instead of just making a reference to the master MP3 in iTunes!!) 