Ripped file format and directory structure

Hello,  

 I have just joined the forum and have been using EAC to rip my audio CDs. The usability of EAC is great. The ripped format is WAV and have used the following Filename configuration which allows me to view the files in the associated Directory structure created.
 

 ARTIST\ALBUM\nn. TrackName.
 

 Having ripped around 200 CDs I have also just moved all the files to my new QNAP NAS. QNAP's native media centre Music Station is however not adding the files to the library. This could be an issue with QNAP itself and may be due to the fact that the folder structure is not supported. Not sure myself and have raised a ticket with QNAP. If QNAP come back with the folder structure being the issue, can I, without having to rip all the CDs again to the appropriate Filename configuration alter the files using EAC or a utility?
 

 Any suggestions from the the forum will be greatly appreciated.
 

 Thanks,
 Rajesh