Disregard this bug, the items reappeared in the chest during one of the roll backs. Not really willing to reproduce it again but basically..
I was crossing a large body of water using a boat. When traveling at top speed of the boat, chunks ahead of me did not load and the boat and I 'fell' into the empty chunk. The chunk did not load after a few moments and I did not die, so I logged out, and logged back in. This occurred a couple times on my journey and by the time I had reached the exchange and opened my inventory the items were missing.