I see several problems with your file. The materials have been removed from the SketchUp file. As you can see in this screen shot, the brick texture, for example, isn’t even present in the SKP file. Although not likely to be related to your problem, you also have exposed reversed faces, not grouping of geometry, and incorrect layer use. (Notice the Layer field in Entity Info is blank meaning the selected entities are scattered on multiple layers. All edges and faces should be on Layer 0.)
You’ve also set up the scenes in your SketchUp model to not save properties that you really should be saving. Different properties to save a deselected for the different scenes. This means that certain changes you’re making in the SKP file won’t get saved into the scenes and thus won’t be translated to LayOut.
Additionally, you’re modifying scenes which you shouldn’t be doing. All four of these selected viewports point to the same scene in the SketchUp file. They should each be pointing to a different scene.
The LayOut file is updating the SketchUp reference before exporting to PDF which is why you are seeing the changes.