The settings thing is likely, I think right now I only reload mod stuff for backwards compatibility when mod version changes. I'll have to add another function for when just mod settings change. Could never reproduce trees being passive on newly made worlds, but ent spawning only happens when a minimal evolution level is reached, maybe that's it?
Considering the disappearing entities, I'm not sure. I have no code that would manually destroy buildings, it's all done by dealing damage. OTOH there is one rare event where a turret would be "subverted" to enemy side, that I assume would not create a ghost after destroying it since the turret is no longer "yours". No clue about walls though.