I was doing Shattered Throne to finish up getting the eggs and Ahamkara bones that I didn't get before, and all of the Ahamkara bones are gone. This wasn't mentioned anywhere in regards to the content vault and its on a planet that isn't being removed so it wouldn't make any sense to take it out of the game. Is this a bug?
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Yes this is a well known issue at the moment, reported from a lot of players but not the only ones in the Dreaming City. Bungie is investigating this issue.