I did a test build of your arrangement and was able to duplicate what you are seeing. It is an issue that has been around a while and your post has been merged into that thread.
From your pics, I think you are building a castle with a perimeter wall that is on a raised foundation. So to make the invisible parts become visible again, you are going to have to break that wall somewhere. Deleting one tile is enough. So I suggest you pick a spot that you can hide with landscaping or an object so you don't ruin the look of what you are building. Another thing you can do, is to scrape the raised foundation and just use a flat foundation.
Hope this helps.
I've had this issue too recently on console (Xbox series S) building a raised Spanish style mansion with high steps on what was the Landgrabbs lot. I was building a bridge from one wing of the house to other and it created a void when I added fences to the high decks and the bridge. I found a workaround by using the "replace" method of building fences instead. When I built fences manually it deleted the foundation. When I used "replace" it added the fences no problem without creating a void where foundations should be.
Thanks for the info. The thing that is happening is that if you use walls on a raised foundation to construct a courtyard the way @pazpacintosh has done, the game will think it is a room. When you delete the floor so you can see the ground again, you get the invisible foundation because the game does not render the foundation wall texture from the inside. You will see this with basements too when the house above is on a raised foundation. There is no texture where the foundation is, so the game makes it see through. It doesn't happen if you use a fence that begins on the ground and is drawn to the house foundation. But you can't use a wall in that case since they won't connect because they are different elevations.
Hope this helps.
