Collections and arrays don't have a special behavior in db4o. When you delete a collection, the collection-members are not deleted. The collection and objects are two independent objects for db4o.
To remove object from a collection you can simple use the regular collection-operations and then store that collection.
PilotGroup group = findGroup(container);
final Pilot pilot = group.getPilots().get(0);
group.getPilots().remove(pilot);
container.store(group.getPilots());
assertEquals(3,allPilots(container).size());
assertEquals(2,group.getPilots().size());
If you want to delete a collection-member, remove it and then delete it.
PilotGroup group = findGroup(container);
final Pilot pilot = group.getPilots().get(0);
group.getPilots().remove(pilot);
container.store(group.getPilots());
container.delete(pilot);
assertEquals(2,allPilots(container).size());
assertEquals(2,group.getPilots().size());