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Only a single Cipher may be held in the inventory at any time.
Normally, Xûr allows only one Fated (Isochronal) Engram purchase per week. Ciphers may be spent on additional Fated Engrams past this weekly limit.
Alternately, Exotics from past content may be purchased at the Monument To Lost Lights; in addition to the Cipher, this also requires Glimmer and one or more Ascendant Shards, plus either Planetary Materials (for non-Raid exotics) or Spoils of Conquest (for Raid exotics).