You have to remove all items from the chest then close it and reinsert all items back in the chest. I find it easier to just drop stuff on the ground in an out of the way area. If you wanted to you could use the various rooms in Heli's bar and store different types of items in each.
From my experience the items never go away. I have a large collection of trash left by the Higardi on the Arnika Road (I am level 20 and the items are worthless to me) and it never goes away.
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