I recommend Sorune as a sync manager. You can get it at
www.sorune.com. While it has (imho) an ugly user interface it's gold under the hood.
For your case, it can scan the Neuros for audio files and then rebuild the Neuros database (as you probably know: if the file is not corretly in the database, it doesn't exist for the Neuros and can't be played).
You could then go on and move audio files manually to the Neuros and just resync the database. Thats how I do it since a long time.
Sorune runs on Windows and Linux alike and unfolds it's real powers on the command line (while you don't have to go into that)
Cheers,
Martin