So I ran into a similar problem. I came over to pc from ps4 cross save. I had 2/4 locks unlocked on my Mysterious Box. The Butterfly, and Handlock key. I noticed that the Key Mould was on my quests page, and I also had a Legendary Pulse rifle frame on the final step. I decided to knock out the forge after I got all 24 watcher lenses and ran Lake of Shadows TEN times back to back to get 200 Glimmering Amethyst. Ran Bergusia, killed the drones, and got my Black Armory key. Used on my box and it disappeared. I'm not angry. I know these things happen. I'm disappointed to have wasted two hours grinding my life away for an exotic I thought was attainable. I really enjoy this game. The community for the most part on both steam and ps4 have been really helpful. Please fix this. I still love ya! Hopefully some of this information helps.