I double checked, and there is only a single copy of the mesh per items. I have just imported the glb and created an "inherited scene" from it.

What about having 2 render systems, one which cares about the DrawOnTop component and another one which will render the non matching entities. Adding or removing this component will just unregister the entity from the system list and vice versa.

thanks for the idea, I have the feeling that a mix between a global GameState and an object layer per chapter will do the trick in my case.

the layer idea sounds really interesting. I am using Tiled as a map editor and all my interactive entities are described in an object layer (baddies, items, light sources, npc etc...), it would be easy to just load the correct object layer based on a "chapter" reference, ie: mapLoader.load('map.tmx', 'chapter1') and then loading the corresponding object layer.