It seems like what is needed is a way to “Update” the imported data without destroying the work you’ve already done. The issue I see with some kind of proxy system is that there may be thousands of objects that you would have to manually re-import each time. The best solution for this case I think of is to have a special command that looks at the data in the scene and the data in the import file and runs a comparison that looks for differences in object geometry and transforms and then only updates those those items leaving the materials and lighting and any other added objects intact.
Actually this is quite useful for all kinds of other things. I’ve often thought of an object importer that stays on the object in a modifier. Whenever the external object is changed you can just hit the update button and it simply updates the verts and transforms. The modifier simply uses the importers that are built into Blender. You could have checkboxes for what to update and what to leave the way it is. But that’s just for single objects. I don’t know what you would put in the scene to handle the updating of an entire scene? Maybe a new type of object that it just an empty with some data on it?
Oh and ejnaren, it’s “Depsgraph” not Debsgraph. 
It’s sort for “dependency graph”. It’s a mechanism for tracking what needs to be updated when you change something in the scene. A faster depsgraph makes working in Blender faster. Esspecially on large scenes and it speeds up things like animating hierarchies and animation playback… In theory at least. I think eventually the devs are also hoping to have a system that can handle a node based system like softimage ICE or Houdini.