I can confirm that it is possible to farm for the cipher without doing the whole thing over. We killed the lvl34 Boss and the cipher dropped for me. His detainment-cages killed my whole fireteam while he was in his death animation and we had to do the round over again. This was a coincidence though.
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You can only get it on your first boss kill each week. Even if u kill the boss and wipe it won't work.