This is a bug I'm still trying to fix, but if you email me (mezezik@gmail.com) your save file (localAppData/ufo50nonograms/nonoSave.ufo), I can help you get the crystal back.
Also, just to help me figure out what caused this, were you targeting puzzles at all?
I'll send you my save file then, thank you very much for reaching out!
As for the puzzles, yes i was. What happened was that i decided to try and get the secret before actually finishing the game, so to optimize my resource gathering i just targeted the games had the least amount of puzzles left, and target every single one of them left in that order. After i unlocked the secret, i focused on finishing it, and when i was done, the crystal disappeared when i clicked it. That's why i revisited the page, to see if there was a fix, and after i updated the game the crystal was still gone. I even tried going to the puzzle list and tried clearing the targets or something but no dice.
That's the only bug i experienced aside from the one when a controller is connected, which someone else already mentioned.