I have also had this occur - exactly as described above. The boulder will not get removed by the Golden Children - I have two of them now, since the 'bug'.
Now that would be something if they could breed - Superman flying around, or something

Since completing the 12 puzzles, after about 180 hours, I returned to the game to keep it ticking over on a daily basis. After about 320 hours I found all the buildings reset. There was definitely no 'event' on that occasion, when I returned to the game.
I had assumed that normal wear and tear had wiped out the buildings (although that didn't explain the stone becoming uncarved. The boulder only returned the day after!