I haven't looked at my villagers for a couple of days (they were on paused) and everything is reset. They are still pushing the statue BUT

The alchemy lab is in shambles...
All the puzzles are back to zero (even though the door keys are in the door)
The trees are gone....

Sniff

Unfortunately, this rare bug was not discovered until several weeks after the game was released. We don't yet have a fix for it, but we are looking into the cause. After you have experienced this bug, we do not recommending starting over. Since this bug does not affect the villagers and their skills, the food supply, or the technologies and tech points, you will be able to have your villagers complete the reverted puzzles fairly quickly.

Although the bug is rare, you can prevent the possibility of a reoccurrence by backing up the savegame files regularly. The procedures for performing a backup can be found here.