Were the files all mp3s? That might have something to do with it.
I remember Napster always had trouble reading files that weren't mp3s. Another issue might be that you could have misplaced certain files to other locations than your designated "MyFiles" folder. Another thing is, the files could be corrupted, or ripped in a new way that Napster simply can't read them anymore, this has actually happened to me before as well.
And I agree with you, Napster 7 thru 10, was the best music player, based on sheer simplicity of design layout and organization of files & file information. I really wish it was still compatible with Windows 7, I seem to be having trouble opening it in 7 outright. Even with all the old tricks I used to use to bypass the reg info. It glitches hopelessly.