Hmmm...so I guess I am not alone here. Well, I have had it happened to me twice. I didn't have the previous saved game, so after the first time my solved puzzles became unsolved, I resolved those that I was allowed to solve again.

2nd time when it happened, I can't solve the spring water and thus the garden. Luckily this time I have been saving my savegame.pdb every few days. So far so good except my boulder is still blocking the cave BUT nobody seems to bother with it. In the game status, it's solved, so I guess the villagers also assumed so.