When the collection is disabled and was only referenced by a node tree, it was missing from the depsgraph. The Geometry Nodes modifier tried to add a relation to it, but it couldn't because the collection was not in the depsgraph in the first place. Now, the collection is always added to the depsgraph when it's referenced by a node tree that's in the depsgraph too. This makes the existing code that adds the relation from the collection to the Geometry Nodes modifier work. Pull Request: https://projects.blender.org/blender/blender/pulls/136328