The function saveList in net.sourceforge.dvb.projectx.gui.CollectionPanel
does not warn before overwriting files. The problem is aggravated by the fact that the same filechooser is used for adding input files to a collection. Under Gtk/Linux (Gtk Look and Feel) this will result in loss of the input file when you just hit OK in the "Save Cutpoints" dialog.
Fix:
add the following lines to saveList()
if ((new File(newfile)).fileExists() && javax.swing.JOptionPane.showConfirmDialog(this, "Overwrite existing file " + theFile + "?") != javax.swing.JOptionPane.YES_OPTION){
return;
}