Do you have "Preserve Scale on Resize" checked (it's in the SketchUp Model Inspector's View tab)? I just tried it with the standard views with ortho projection, and when I changed the scale on each scene, it added "(Modified)" in front of each of the scene names, but did NOT change the scaling when I changed geometry and materials.
I may not be doing thing exactly the way you are, so here's what I did: I created a simple SketchUp model with 7 scenes, each with Camera->Parallel Projection, and the 7 views you get from Camera->Standard Views. I sent this to layout, and created 7 pages, each with a page matching the name of the view (top, bottom, etc...) and changed the scale to 1/4" = 1' (1:48) on each page. Preserve scale on resize was checked.
I then went back to SketchUp and changed a few things (geometry of building, materials, etc...), updated a scene, saved, then back to LayOut and updated the skp model reference. Everything stayed the same for me. More info if you can, because if this is happening, I can see how it would be a pain.
b