I just had a small brainwave regarding the lights! My lights are actually part of a blueprint (I use a mix of static and stationary versions to get the effect I want - the stationary one flickers a bit).
When I create a prefab with a normal point-light and my blueprint ‘flickering light’, duplicating the blueprint stops the blueprint-light working while the normal-point-light continues to work.
So, there’s an issue with lights components in blueprints that are part of prefabs - they can work, but seemingly only once they have been adjusted after the prefab has been placed. This adjustment only needs to happen once for it to be permanently okay, but duplicates need it to be done again.