Well, it doesn't really delete them, let me elaborate.
I am using beta 13 and The latest Hijack.
If I hit down down down I get a running total of 7769 tracks,
which is the EXACT number of tracks I have uploaded to the player.
No song appears in more than one playlist.

Then If I switch to the "Random" or "least recenlty played" shuffle mode (those are the only 2 I tested)
then there are only 7753 songs in the total running playlist.
If I switch Shuffle off, I'm back to 7769 tracks......

What gives ?