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I haven't worked with 3d models in a year or so, but gltf was the way to go for me at the time.
The reason the saved scenes done get updated is because you're actually saving them as a physically separate file when you export the branch to a new scene. There is no workaround for that since you're making a physical copy of the data and storing it in a different place on the hard drive.
What about modifying the importer to automatically export each branch to a new scene?
A few things to note there:
That importer is probably part of the engine code, probably in C++, and if it is it will require recompiling the engine and using your custom build for your game.
From the docs on 3D importing:
.blend(Blender). This works by calling Blender to export to glTF in a transparent manner (requires Blender to be installed).
So it looks like the blender importer is already using the (recommended) gltf format anyway.
There is the Godot Blender Exporter which you may find useful instead.
You can write a tool script that extends EditorPostImport and do things with the scene on import without having to modify engine code. I've used this to great effect on gltf files.
EditorPostImport sounds promising. Hopefully I can make it save the branches or update them if they already exist. Thanks!
When you export each section as a new scene, you're saving it as it's own individual object, no longer connected to the .blend file.
There is are two work arounds, both are a bit cumbersome
You can keep the .blend file saved in a scene, click the mesh node, copy the value, then paste the value onto the instantiated/local mesh node. This doesn't update each file automatically, but it's easy enough to keep everything stored locally and move things around as necessary.
Use the Linked library addon in Blender to be able to have a main blender file, but you'll still need to save each individual object as a .blend and import it into Godot. The benefit of this is that you can edit the files rather quickly, without needing to manually open each file. It's an Addon that needs to be enabled, then you need to go to file>Link>collections and add your objects from there. The only real benefit of this, again, is having one .blend file you focus on in blender.
I use a mix of both depending on what I'm doing but predominantly use method 2. This updates each object automatically in Godot
You can also write a tool script to automatically replace the mesh when it's updated, I haven't done this but it's technically possible
Thanks I think I should be able to work something out with EditorPostImport to export the branches/update them if they exist.