I had a similar issue when I leveled the ground to build a large house with a connecting craft area. The next night and there is a pi;e of ground almost blocking the door, so i level it down and the next day it is back. I leveled it again but used a pick to knock it down before using the how. It has not returned.

https://steamcommunity.com/sharedfiles/filedetails/?id=2554355689