Hi again, guys!
Thanks for your comments!
I’m pretty sure I’ve found the root of my problem:
the support for the roof that kept disappearing was, among other building pieces, a bunch of pillars. These pillars where placed in between two floors, where the tiles did not match position - i.e. wedged ceiling pieces would be directly above square ceiling pieces under them, etc.
The pillars could be placed in between the two floors just fine, but they stood “askew”, not solidly in the middle of the floor tiles beneath them.
It seemed the pillars would sometimes “flicker” between “understanding” which tile they where attached to. Generally, the pillars “behaved” like they were placed on the building piece under them, carrying the same stability. But then, in brief moments, they would seem to “behave” like they where attached to the tile above them, ignoring the piece beneath them - and as a result, their stability would drop drastically for just a few moments. This drop in stability would “ripple” up through the building pieces they were supposed to support.
My solution was to place new pillars - and place the solidly on the building pieces they stood upon.
This means that the upper of the two floors no longer looks the way I want it to, but it’s better than rebuilding the top of my roof every day.
The lesson I learned from this: don’t mismatch tiles between two floors … stability will start to behave weirdly.