iTunes manages the overall structure of my files. I added a number of discs to iTunes. No problem, they showed up ok and played fine in Subsonic.
I generally dislike Genre tags and periodically wipe them out. I removed the Genre tag from around 10 discs in iTunes and that's when the an issue became apparent.
The albums still showed up in Subsonic but they would show no tracks - just what appeared to be empty folders. I tried adding back the same genre information that was removed and then maybe 1 track would show up.
In the end I just renamed the album folder to something else and then back again and the tracks showed up. SS retained the play count but I'd lost any favorites I'd tagged.
I've wiped out genre information in bulk before and not seen this behavior and it seems a little odd.