I just updated the game to address a problem pointed out by a player. It seems, if you entered a cave, then died before leaving the cave, items like crystals and minerals that appeared in the cave on your first visit would no longer be there if you reloaded the game and went back. Furthermore, any crystals or items you picked up would also have disappeared from your inventory.
This is a big problem, but it is something I actually addressed in a previous update ... or so I thought. In fact, I did create the functionality for items to be saved properly, but I only implemented it for treasure chests. I had somehow forgotten to add the code to the crystal and mineral objects.
4.1 addresses this issue, and from now on any caves you discover and die in, should reload with the same items in place.
It will not, unfortunately, fix caves where this problem has already occurred in an existing game.