Bungie meanwhile offers a short term fix for raid keys disappearing from one’s inventory.
Bungie has been keeping busy behind the scenes with Destiny 2. Along with outlining various aspects of the Faction Rally and discussing weapon balance in the coming days, it also dropped some patch notes for its upcoming hotfix 126.96.36.199.
Such issues like clan engrams only awarding Trials of the Nine and raid gear 10 Power (which didn’t seem like a bug at first) and progress for the Exotic Quest “His Highness’s Seal” which is necessary for the Legend of Acrius shotgun will be fixed. Also, that one issue which causes players to be killed continuously in the raid if an encounter was failed and completed at the same time will also be fixed.
Keep in mind that these are only some of the changes that players can expect. More will likely be on the way. As for the case of Leviathan raid keys disappearing, Bungie has advised signing in with all characters or inspect them via the Destiny Companion App after the weekly reset and before attempting the raid. A more permanent fix is likely in the works.