Pffff, my current build is driving me crazy. Making small changes gets rid of all kinds of stuff that haven't got anything to do with it :s
https://38.media.tumblr.com/4aacd3957236c8733e2e5c94bff81807/tumblr_nf9qiamCjZ1s873l7o1_400.jpg
I'm about to paint the interior of that little tower, and it gets rid of both doors AND a pillar that isn't even on the same level. And that's just the little tower. When I'm done painting the entire interior, I can probably start all over again, re-applying windows and door and pillars and whatnot. It also happened when I extended the foundation near the entrance (ground floor), aside from some doors connected to the foundation, it also deleted a couple of pillars on the third floor.
I'm guessing it has something to do with enlarged objects bugging things? I almost never use enlarged objects, and I doubt I ever will again once I finish this piece :p