Log off/on always makes the item re-appear. Hopefully this works for you as well. And apologies for not reporting this myself the first time I saw it.
I've had items appear to disappear three or four times. It seems to randomly (and very rarely) happen when multiple events are occurring as you move the item. Doesn't appear tied to gear changes. For me it has occurred during gathering/crafting while moving inventory from bag to BP or reverse.
Happened to me only once since the game went live. A couple of weeks ago I was foraging while moving an item from BP to bag when I was attacked by a mob. Dropped the item in bag, when fight finished it was nowhere. After relog, there it was exactly where I put it.
Edited by Irradiated, 17 December 2013 - 10:49.