The issue was caused by light and shadow linking runtime data not evaluated first time for lights linked to scene indirectly. Simple solution is to hook up shading component to the instance operation, so that visibility flag is properly propagated to the shading component, and the light linking is evaluated. Do it as non-flushing operation to prevent possible unwanted re-evaluated of instancers. Pull Request: https://projects.blender.org/blender/blender/pulls/117301