Commentaries removed from that section of the PG return to the list when a new passage is entered or when PG is regenerated after restarting L4.
Comment from MJ Smith: I believe this is only a bug on a restart but the correct behavior on a change of passage.
Software version: 4.0b SR-2, 4.0c.
Reported by Dave Hooton.
Forum link: http://community.logos.com/forums/t/16572.aspx
Status: by-design Guide must be saved by entering Title in top reference section.