I had the same issue the other week. I lost my Atheons Epilogue when I moved it from the Vault to my Hunter while sitting in Orbit. I closed the game and app completely (don't know if this actually helped) and still couldn't find it. After about twenty minutes of frustration, I logged in as my Warlock and for some reason it was in his inventory. But when I checked his inventory on the App, it wouldn't show up. It wouldn't show up on the App until I equipped it.