File Output Node doing nothing due to TREE OF NODES being associated with unused scen

When I had a chain of nodes stemming from one RenderLayers node, it worked.
But now I have different scenes composited on each other with blend modes (Mix Node).

The TREE OF NODES is associated with an unused scene.
In other words when I open a scene that IS used in the TREE OF NODES and click render, the File Outputnode does nothing because TREE OF NODES is part of a different scene (even though it refers to multiple scenes hence multiple RenderLayers ‚Äčnodes)