I got the following exception when I tried to delete all the items from my "refs=0" search:

java.lang.NullPointerException
at org.jempeg.empeg.nodestore.FIDPlaylist.shouldRefCount(FIDPlaylist.java:784)
at org.jempeg.empeg.nodestore.FIDPlaylist.removeFID(FIDPlaylist.java:867)
at org.jempeg.empeg.nodestore.FIDPlaylist.removeNode(FIDPlaylist.java:496)
at org.jempeg.empeg.model.AbstractPlaylistNodeModifier.removeChild(AbstractPlaylistNodeModifier.java:246)
at org.jempeg.empeg.soup.SearchSoupUpdater.nodeRemoved(SearchSoupUpdater.java:175)
at org.jempeg.empeg.soup.SoupUpdateNotifier.nodeRemoved(SoupUpdateNotifier.java:52)
at org.jempeg.empeg.nodestore.PlayerDatabase.fireNodeRemoved(PlayerDatabase.java:547)
at org.jempeg.empeg.nodestore.PlayerDatabase.removeFID(PlayerDatabase.java:486)
at org.jempeg.empeg.nodestore.AbstractFIDNode.delete(AbstractFIDNode.java:259)
at org.jempeg.empeg.model.SoupPlaylistNodeModifier.delete(SoupPlaylistNodeModifier.java:73)
at org.jempeg.empeg.emplode.action.DeleteAction.actionPerformed(DeleteAction.java:61)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1450)
at javax.swing.AbstractButton$ForwardActionEvents.actionPerformed(AbstractButton.java:1504)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:378)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:250)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:216)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:230)
at java.awt.Component.processMouseEvent(Component.java:3715)
at java.awt.Component.processEvent(Component.java:3544)
at java.awt.Container.processEvent(Container.java:1164)
at java.awt.Component.dispatchEventImpl(Component.java:2593)
at java.awt.Container.dispatchEventImpl(Container.java:1213)
at java.awt.Component.dispatchEvent(Component.java:2497)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:2451)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:2216)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:2125)
at java.awt.Container.dispatchEventImpl(Container.java:1200)
at java.awt.Window.dispatchEventImpl(Window.java:914)
at java.awt.Component.dispatchEvent(Component.java:2497)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:339)
at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:131)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:98)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:85)
Exception occurred during event dispatching:
java.lang.NullPointerException
at org.jempeg.empeg.emplode.ui.PlaylistTableCellRenderer.getTableCellRendererComponent(PlaylistTableCellRenderer.java:73)
at javax.swing.JTable.prepareRenderer(JTable.java:3540)
at javax.swing.plaf.basic.BasicTableUI.paintCell(BasicTableUI.java:995)
at javax.swing.plaf.basic.BasicTableUI.paintCells(BasicTableUI.java:917)
at javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:858)
at javax.swing.plaf.ComponentUI.update(ComponentUI.java:39)
at javax.swing.JComponent.paintComponent(JComponent.java:395)
at javax.swing.JComponent.paint(JComponent.java:687)
at javax.swing.JComponent.paintChildren(JComponent.java:498)
at javax.swing.JComponent.paint(JComponent.java:696)
at javax.swing.JViewport.paint(JViewport.java:668)
at javax.swing.JComponent.paintChildren(JComponent.java:498)
at javax.swing.JComponent.paint(JComponent.java:696)
at javax.swing.JComponent.paintChildren(JComponent.java:498)
at javax.swing.JSplitPane.paintChildren(JSplitPane.java:1006)
at javax.swing.JComponent.paint(JComponent.java:696)
at javax.swing.JComponent.paintChildren(JComponent.java:498)
at javax.swing.JComponent.paint(JComponent.java:696)
at javax.swing.JComponent.paintChildren(JComponent.java:498)
at javax.swing.JComponent.paint(JComponent.java:696)
at javax.swing.JLayeredPane.paint(JLayeredPane.java:546)
at javax.swing.JComponent.paintChildren(JComponent.java:498)
at javax.swing.JComponent.paint(JComponent.java:669)
at java.awt.GraphicsCallback$PaintCallback.run(GraphicsCallback.java:23)
at sun.awt.SunGraphicsCallback.runOneComponent(SunGraphicsCallback.java:54)
at sun.awt.SunGraphicsCallback.runComponents(SunGraphicsCallback.java:91)
at java.awt.Container.paint(Container.java:960)
at sun.awt.RepaintArea.paint(RepaintArea.java:298)
at sun.awt.motif.MComponentPeer.handleEvent(MComponentPeer.java:349)
at java.awt.Component.dispatchEventImpl(Component.java:2663)
at java.awt.Container.dispatchEventImpl(Container.java:1213)
at java.awt.Window.dispatchEventImpl(Window.java:914)
at java.awt.Component.dispatchEvent(Component.java:2497)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:339)
at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:131)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:98)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:85)

It's repeated every redraw if the Playlists pane is selected on the left. No exception when Search is selected. It's also fine when the Playlists pane is present, but the search containing the deleted items is not highlighted.

I get the exception when any soup that contained the deleted items is highlighted. And the items never get deleted when synchronising. I managed to remove them by copying them to another playlist, then removing completely, but it ought to work from the soup directly.

Perhaps this is related to your Known Issue no. 1, in that changing the refs of an item in a refs-based soup does Odd Things?