I had the exotic bounty for Bad Juju prior to the patch, and when I logged in after patch went live it was no longer in my inventory. My elder cipher bounty is still there, but not the other exotic one. I can only assume that this is a bug, and was not intended, as it can take quite a while for those exotic bounties to become available to you.
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Edited by KannibalKlown: 9/11/2015 6:05:28 PMGo,to,the speaker. He should have it Happened to me and others. It's by design. exotic bounties were auto completed. But except for,elder cypher, all quest icons were removed so you have to go to the speaker for the thorn, gun smith for bad juju, and I don't know where else for,the others. Elder cypher is still variks