Performance issues while decomposing large game object

I'm going through the process of moving some scene objects into a prefab. I started by creating an empty "map" and then dragging all of the level geometry into it, and then dragging that "map" empty to create a prefab.

I then planned to turn most of the nested game objects into nested prefabs, which is what I'm in the process of doing now.

The problem I'm facing is that dragging a nested game object out of my "map" prefab is very slow. Each prefab I attempt to create this way takes about 2 minutes.

I tried to Profile the editor when this happens, but dragging the nested game object into the project hierarchy puts unity into a non responsive state while it's happening, and the profiler doesn't update.

Any ideas on how to prefabify my objects in a less painful way and/or how to profile the editor in this situation?

I'm on 2018.3.0b5.

 

I'm just curious: how many GOs embedded into each other? And why is it useful to include all of the level geometry in one prefab? Are you planning to use the entire level multiple times? Or what is your logic behind this move?

 

The idea was to use prefabs like we might have used multi-scenes before: level designer can work in one level using some custom objects and then I could drag and drop the geometry prefab into a different scene.

That said, I'm really just trying to find efficient ways to use the new prefab system, so if this is a bad idea or there's a better one, I'd love to hear it.

 

Oh, and to answer you other question, I didn't count them but there was a lot. It was a ProBuilder constructed greybox level, so there was a lot of unoptimized meshes and game objects floating around.