@mikes1987
I agree with @Chazzzy , not sure exactly what you're problem is. My guess is trying to remove the floor/ceiling on the stairs side after raising the foundation to go to the basement (first underground level).
This has nothing to do with updates or a broken game or even mods. It's the build mode mechanics. Which can be frustrating at times, I know. ;) My guess is what @Camkat said, either remove the ceiling/floor first before raising the main level, and/or putting in the stairs.
I'll give it a try, maybe I can help. I suppose I could make a video, but I'll just take screenshots for now.