Good guess, I do get 99% of my music online, which causes some incompleteness as far as cohesive albums are concerned. I'm also getting new music all the time, and phasing out old music, so the main operations I do are:

1) add a new song/album to my New Music directory
2) decide I like a song/album enough to move it to my Rotation directory
3) decide I don't like a song/album and delete it from New Music
4) get sick of hearing a song/album and remove it from Rotation, but back it up on CD.

obviously, the only easy step right now is #1. I use directories because:

1) it's conceptually simple
2) it let's me use the same organization on my ipod
3) I also access my mp3's via file sharing from work, so similar organization helps there too

I would delete everything and resynch, uploading everything again overnight, but I would fear reducing the rio hard drive's time to failure.