That is strange...
Try deleting all of the files in the '..\Divine Divinity\Run\Dynamic' folder, then start the game, load your latest save and check the chest.
The Dynamic folder is used as a cache for the game. Files are created / copied there from the save game folder when you load, and written / copied from that folder when you save a game. The files will be re-created as required the next time you start Divinity. If there was a corrupt file in that folder, deleting the files should fix the problem.


There is a way to replace quest items.

Lost Items - guide and directory of inventory files


A couple people have had problems with chests (weight bug and disappearing chests - broken links are fixed in a reply), but vanishing contents are pretty rare (except if you place items in the chest in Malcolm's house in Verdistis before finishing the quest that seals the house, which unfortunately also clears the chest contents).


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