Level flags and level-flag-like things such as Sokoban rules should be tied to wardstones, a new type of gray stone. If there is no wardstone providing a level rule anywhere on the level, those rules no longer exist on that level.

Removing the gray stone from the level where it generated shatters it. However, the player can also cancel a wardstone, in which case moving it will not shatter; there should also possibly be a way for the player to reapply the same or different “enchantment” on a wardstone which will then start enforcing that level rule on whatever level it’s activated on.