I put all 5 of my crystals in a box and took them down to that crystal hatch thing when i realized that my earth crystal was gone. i went back up to see if i dropped it or something but i couldnt find it and i think it is just missing, so i restarted my game to see if it would respawn or something to no avail, but when i went back down to the crystal door i couldnt even do it, because the dungeon was sealed again even after me already opening it and the sword still being in the shrine

Edit: I reset crystals with the slipcor save fixer, and all other crystals besides earth are fixed. The sword is still in the shrine and the dungeon door is still closed