So my cipher bounty still isn't working, but I heard that you had to kill Skolas again. Can someone give me confirmation on whether or not this works.
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I have the same problem. I can confirm that bungie's comment that you need to defeat skolas to get the bounty is full of crap. I have defeated skolas but did not get the bounty fixed. I even made sure that I had 2 slots open. So I am guessing they just mean that you have be lucky enough to get the cipher again and then you will get two ciphers at the same time, but it will actually only count as one. Thanks Bungie for nothing!