This happens to me very occasionally, and deleting those sections have never caused any issues. One of the houses it happened on was my Dynasty house. It only happened once, when I was first building it. That game is still going on, and works just fine. It also happened a couple of times on my first legacy house, and I deleted them and went on with the game. The reason I don't have that save anymore has nothing to do with glitches, bugs or file corruption. The hard drive it was on burned out, and I wasn't maintaining backups on a flash drive like I do now. But before that hard drive burned out, I played that particular family for 9 generations.
Likewise, I have built probably more than 100 houses since the base game came out, and those are the only times it's happened. I wouldn't be telling you that you had nothing to worry about if I thought there was even the slightest chance that there was something to worry about. In my experience, while it's a rare occurrence, this is just something that happens. The chances are really good that if you delete those sections, it will be a long time before you see something like that again...if you ever do.