No one will believe me, but I'm going to post anyway hoping that bungie will help. I just got a gjallarhorn doing roc strikes and I wanted to level it up using my hunter, so I was on my hunter and transferred the gjallarhorn using the app and it disappeared. I'm not lying cause I have the grimoire card and 0 kills.
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Well, if you actually had it, then you probably didn't lose it. Today I had the same problem with Thunderlord. I was trying to upgrade it Xur, but it wasn't in my warlocks inventory after I moved it with the app, but in the app it said it was. I fixed it by moving it(in the app) off my warlock, to the vault, and back to my warlock. Fixed it!