I don't suggest you use one drive to work between two rekordbox installations on different operating systems, but it sounds like you're just adding audio files to the drive on one machine and rekordbox on the other.
rekordbox itself doesn't add anything to the audio file (other than modifying the metadata). The playlist, waveform overviews, artwork, etc. are all stored in the database and accompanying folders.
Don't import/export to the same device, that will only create confusion and duplication.