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I had Cipher: Shantotto II in my inventory and went to change my job to BLM and then warped to Windurst to go and trade it in for the trust, but when the trade window opened, the cipher was just gone from my inventory and I had nothing to trade him. I searched all my storage and it just poofed out of existence. I know I didn't drop it or anything. I did talk to Wetata before attempting a trade but I checked my trusts and she's not there, either, so something's for sure gone wrong.
Check the mystic retriever point in windurst woods next to trust npc
Also check your other bags. Items don't just disappear without you actually trading them, throwing them away, or selling them.
You can also use /itemsearch "Cipher: Shantotto II" and the game will tell you where it is. If it's not in any non-NPC storage system this will confirm it.
There's also a somewhat recently added trash can feature that will allow you to retrieve items you accidentally toss (this list is forgotten when you change areas, so it only works right after you toss something), so if you do accidentally throw something away it is possible to recover it if you do so right away.