Did your files disappear from the NAS, or just from the library ?
If you restored a Unix backup on a Windows machine, it could be just that the name of the files, as seen from your computer, has changed (e.g. /nas/music/file1.flac to M:\music\file1.flac).
In that case, if JRiver does not find the files with their old names, it could just have removed them from the library, while still leaving them on the NAS.
Just a suggestion...
CM