I just realized that when I watched the video, I skipped through it to see if it was the same bug I was already aware of. The fix in v1.6 addressed the closed door in the first room of the dungeon, but I have no idea why you lost the crystal. If anybody experiences that again in v1.6, please let me know, and please try to recall exactly what you did as closely as possible from the time you got the crystal to the time you reloaded and discovered that the crystal was missing. It's possible that the two issues were related, but they could also be two separate issues, and if that's the case, then the crystal could still be bugged.
Also, for future reference, contact me for support, not Conn. I credited him because I used a lot of his code, but he is not directly related to the project, and will most likely direct you to me for support if you do try to contact him.
And if anybody comes across this in the future experiencing the same issue because you're using an older build, here are the relevant cheat codes:
Unlock the door: 7EF05181
Have crystals 1+2: 7EF37A03
Load your game, enable the cheats, save your game, disable the cheats. This should fix your save file. However, if you continue using the older ROM, it will re-trigger the bug and you'll have to do it again. If you update to the fixed ROM, the fix should be permanent once you save the game with the cheats on.