I have just tested and my crystal is still gone =(
Is there a way for me to continue without starting over?
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.