OpenGL is not a scene graph. It's simply a drawing API. There is no internal representation of what's visible on the screen. The only thing OpenGL is left with after drawing something are the contents of the framebuffer(s).
You want something changed, you clear the framebuffer and redraw your scene with the adjustments done.
Regarding Quation EDIT 2:
I can only reiterate my first statement: OpenGL is not a scene graph, i.e. you don't "build" a scene with it. What you have is geometry data (vertices) and sampling data (images/textures).
Then you have a drawing function, that tells OpenGL to make triangles, lines or points out of the geometry data and fill the fragments generated (=pixels) with values derived from illumination calculations, solid colour and texture sampling data.
Making a change to a scene does not happen in OpenGL! Making a change in the scene happens by making the changes in the geometry data supplied to OpenGL and the different drawing operations this implies.
Like I already said, you don't "build" your scene/geometry with OpenGL. You use a 3D modelling program like Blender, Maya, 3DS Max, Cinema 4D or similar for this, store the model to some data store (file, web resource, database entry, whatever) in a format your rendering program can access. A changed model is stored in a different storage location, loaded as well and to represent the change you draw the new model.
Another way to build geometry is using Constructive (Solid) Geometry (CSG) system, with which you build a scene from basic building blocks (planes, spheres, cones, closed surface patches) and logical operations (union, difference, intersection, exclusion). However OpenGL is not a geometry processing library.
What OpenGL gives you are drawing tools: Canvases (=framebuffers), Stencils, Scissors, Collage Images (textures), "Shapes" (=Primitives, i.e. points, lines, triangles) and "Smart Brushes" (shaders). Interestingly enough, by using the stencil buffer with multiple passes one can do screen space, image based logical operations on solids. But this is really just a image based effect and won't process the geometry itself.