Firstly, in Document Properties/Mesh you can choose “Smooth and Slow” or “Fast and Jaggy,” or custom settings. I am not sure how this will affect linked blocks, if the settings are different, Rhino may or may not remesh them. If it does try to remesh a file as large as yours, it will take a very long time, and if it does want to remesh it, then you saved the files normally, and in that case, it might be better to change the meshing on the linked blocks instead, so it will not have to be calculated every time.
[I always save small, so it only takes a few coffee sips to load a 50MB file. BTW, 7-zipped Rhino saved small files give you an fantastic 80% compression ratio! You can save a lot of version like that.]
You can override a mesh on a particular object by selecting it, F3 to get the properties, and you should see “Render Mesh Settings,” there you can also change the settings, from there.
Although it might be tedious, perhaps ReplaceBlock might let you swap blocks. You can create placeholders for your factory areas, machinery, or systems, and keep them in your main file on load, and when you want to work on an area ReplaceBlock the placeholder/imposter with the real section. For this to work, Rhino would have to not load a block that has no instances.
Basically Rhino has the basic functionality to do swaps, but the block manager isn’t written for it, but if someone where handy with scripting they could write a toggle function that uses a special character sequence or extension…
You can also place factory areas on separate layers, and turn them on/off, but you have to be careful as there are a lot of gotchas with blocks and layers.