So I painfully discovered something the other day... apparently (unlike the green or blue engrams) if you have multiple legendary engrams that are the same (such as two legendary helmet engrams) and you try to decrypt them at the same time, it will only decrypt one and you'll lose the 2nd one. So keep them in your vault and decrypt them one at a time.
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I do this all the time, no problem. If it happens again, record it. Are you sure you didn't just get energy, a mote of light, or a strange coin? It's not always an item you know...