so the two musicbee playlists refer to 2 physically separate files but those 2 files have the same track details (artist, album, track number etc)?
In any case, even if there is only 1 instance of the file on the device I see no reason for MB not to write that files' location to the 2nd playlist. Its certainly not something I can recall anyone claiming before.
I wont spend any time looking at this unless some more solid evidence is provided