@dave r said:

OK. I think you already know this but I'll put it out there. SketchUp is not designed as a 2D drawing tool. When there multiple faces at the same height the graphics card has to decide which one should be in front of which and it often gets it wrong. The solution is to work in 3D so the graphic card doesn't get confused. Here I've moved the windows down 100 mm from the walls.
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You wrote the the edges on the window had been deleted but that's not correct. If they had been deleted there's be no faces. The faces of the window end up occluding the edges of the opening in the wall.

With the windows moved down and the reference updated in LayOut the heavier edges for the wall show as desired.
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I've worked with a lot of students over the years who have been assigned to create 2D drawings in SketchUp and who have run into similar issues. Rug and furniture outlines disappearing in their plan views, case work disappearing in their 2D elevation drawings ... I also see students being taught to draw 2D elevations along with their 2D plans in SketchUp. It seems to me that it would make sense to use a 2D drawing application for making 2D drawings if only 2D drawings are required. LayOut can be used that way. Or get the students thinking in 3D much earlier in the process. They do have to learn about making things like section cuts to show plan and interior elevations but there's no chance of making elevations and plans that conflict like there is when making the individual 2D views. And it's more like what they'll do in the real world.

Off topic but something you should pass on to the student. Make sure tag usage is correct. ALL edges and faces should be kept untagged. Only groups and components should be given tags.
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And purging unused stuff periodically helps to keep the file size down and performance up.
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This isn't a huge file but the same ideas apply. Purging unused stuff from this model reduced the file size by 87.5%

Hopefully that all works for you.

Thanks for your detailed response, Dave. I hear what you're saying about the 2D/3D, but this is how it's taught at the moment and so I need to be able to support it.

That's odd about the faces still being there. Maybe I uploaded the wrong file. I've played with it so much I may haven't uploaded the version without the edges and face on the window - the version I have has no edge or faces.

I know how to workaround it several ways, such as moving the symbol down along the blue axis, I just couldn't work out why it was happening if there was no edge or face on the window.

Thanks very much for taking the time to look at it.