Relevant FAQ entries theoretically would be:

Why is the song count different when I shuffle?

What is this 'Soup View' I hear other people talking about?

How can I be sure that I've deleted all copies of a given song?
(Which I just updated to include information about the checkbox prompt, although it what it said before the update was still true.)

However, now that it's being discussed, I realize I'm not certain about one aspect of Emplode's behavior, and I'll ask this openly to the Empeg guys:

Back in the old days, we had "unattached items". Now, we have "soup". Is it possible for a song to be on the player without being in the soup? In other words, could a refs=0 search theoretically find stuff that doesn't show up in the soup? I didn't think that was possible.