Good question. I have the same problems. If I have PE cuts on my end panels and decide to remove or add a toe kick, all my end panel PE cuts get deleted. I'm not sure why this happens. Maybe Clint can explain?
Sorry was on the road and usually just check forums for emergencies when I'm traveling.
When a toe kick is removed, the configuration of the ends are changed losing or adding data for boundary locations. The part editor cuts reference these locations so they must be removed to reset the part.
Not to say that something cannot be done about this, but that is how the software currently operates.