Download the zip at the bottom to checkout the reproduceable example project. This project is a short setup I created specifically to demonstrate essentially what I am trying to do. I will assume you can open the project and hence reference nodes/stuff from it in the below explanation.
I am creating scene instances and adding them into my scene tree through code, those scenes themselves will add other scenes to the scene tree also through code. As in the project, I have a main scene, which on ready adds a instance of the child scene, which has a child spatial node with a script that creates an instance of the grandchild scene and adds that as a child. This grandchild has a event handler such that when the mouse key is pressed it adds a cube mesh instance.
If I first press the mouse key, the cube appears. Now if I try to save the root scene with all the child nodes having set their owner to the root node, the resulting packed scene does not have the cube mesh. If I run the saved scene I simply see empty space. I would like the cube to actually get saved as well as it is part of the scene tree and I am setting the owner to the node that is being packed and saved.
Any help is greatly appreciated.