Perhaps a warning box (which can be disabled) when one updates a scene SketchUp knows is used in Layout.
Or perhaps merely a warning to confirm the update in case the scene is used in Layout.
Or perhaps a warning generated by a user activated checkbox for those scenes that one has selected for use in in Layout
Yes I did this and it messed up my Layout drawing. It is fixable (undo in SketchUp), if you catch it right away. If you go too far, you end up undoing more than you want. And if you saved the model, it is quite painful.
It is hard to idiot proof (ha) SketchUp, but warnings about actions that really mess up the interface to Layout would help.