You are not using Layers appropriately.
Hence these issues...
You should always model all of your 'raw' geometry - lines/faces - on the special default 'Layer0' [this should always be the
de facto 'active-layer'] - and never assign other layers to them.
Later on if you want to control their visibility you need to make them into a group [or component], then assign that group a layer, so then switching that layer ON/OFF affects the geometry's visibility.
Doing it your way - by giving faces, edges etc their different own layers - leads to unexpected consequences - e.g. having a face on an OFF layer hides it - but the when you erase one of its still visible edges and switch the face's layer back ON - that face is gone, because it relied on that now vanished edge...
In this very case some smoothed [non-visible] edges are left on Layer0 while their faces were moved to another layer...
You
do not use Layers in Sketchup like in CAD: layers only control objects' visibility, they do not Lock or Freeze objects, so interconnected objects like faces and their edges should never straddle layers...
You
can use layers to control the visibility of groups/component-instances, AND you can also 'Lock' these kinds of objects so that they can't be accidentally Selected, Moved or Erased.
So to recap -
never layer 'raw' geometry like faces or edges - always group/componentize it, then layer that object as desired.
The only time you should think about using a layer other that 'Layer0 for any basic 'drawing-elements' is for things like Text, Dimensions, Guides etc, which you might want layering to control their visibility for various reasons - e.g. in certain scene-tabs or whilst doing certain kinds of modeling... because these are not dependent on other geometry etc then having them layered is 'safe'...
