Ok so I finally got an error message that helped:
5309.06][660]LogUObjectHash:Warning: Ambiguous search, could be BlueprintGeneratedClass /Temp/Diff/Temp-2-Rev-489-BASE_SeedCluster.BASE_SeedCluster_C or BlueprintGeneratedClass /Game/Seeds/BASE_SeedCluster.BASE_SeedCluster_C
I did a search on the drive and discovered that Unreal keeps a saved version of diffed blueprints, and then for some reason decides to refer to it in the class dropdowns (say for find all actors of class: node). This has to be a bug, at least in the fact that the saved diff version isn’t renamed in some way to indicate its status.