Maybe exit and reload your game a couple of times.
I had previously "lost" part of my thieves guild armour, which I specifically left in Breezehome for safekeeping, to avoid losing or selling it and breaking my thieves guild quest-line. When I went back to breezehome, and checked where it was stored, everything was there EXCEPT my thieves guild hood. I sat questioning myself and wondering if I somehow sold it off, or dropped it, even though I KNEW I specifically stored those items, in that drawer, specifically for safe-keeping.
Then....
Next time I laoded my game, I looked in said drawer, and there was the thieves guild hood, sitting by itself. After assuming I had lost or sold it somehow, the hood actually just magically reappeared in the drawer next time I loaded my game.
So yeah, at least try reloading your game once or twice. They may magically reappear!