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You're spot on, exactly >because< it always respawned at the same time it now will not - because the game did not SAVE the location, it simply always spawned them in on its own - on the new version, it tries to load the last known position, but it has not been saved in 0.0.81 sooo it does not work :O

So when you start a game, the new default game will ONCE spawn them in and THEN SAVE them, so they will not disappear again --

However I had it happen to me that the dark crystal was pushed in a wall by me and then it was gone :P