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whenever I adjust my mesh, or import a new one from Blender, I have to recreate the collisionshape
You do not need to add a CollisionShape3D right away. You can finish adjusting your Mesh first then create the CollisionShape3D at the end.
so it has two meshes. But the collision shape generator ignores the the child mesh
First, move your meshes to this:
Tree
-MeshInstance3D (green part)
-MeshInstance3D2 (brown part)
You then can SHIFT select both meshes and do the create collision sibling.
However, I found that it will create both collisionshapes at the last selected mesh's origin. You have to move one of them to match your other mesh. (I'm using Godot 4.3)