I have been manually trying to get rid of invalid residues on 690 and what I have noticed on several segments is that as I change the side chain to an approved one sometimes the list changes. I will attach two images showing the difference; BTW this change in the list occurs without my shaking or wiggling; all I have done is mutate the side chain which is seg 10.
Not a bug. Tamirh has said elsewhere that changing sidechains may change what is considered surface and core. Your smaller sidechain has exposed the interior, and your segment is now considered intermediate and not core.
Also, if you don't disable filters, restore (recent) best tends to save states right on the edge of losing points, so this situation is more common than a random sampling of game states.