Sometimes items appear to disappear from containers if you have already put a lot of items into that container. This is merely a display bug, however: if you start removing other items from the container the missing item(s) will reappear. Also, if you "Take All" items the missing items will still be added to your inventory. Saving the game while in the same zone as the container then reloading the save will often make all the missing items reappear; leaving the room, or looking in other containers after reloading, will break the container again.
This glitch seems to be caused by an error in the recorded number of items stored in the container. It looks like that number sometimes becomes less than the actual number of items stored. This causes the most recently added items to not be listed in the container's inventory. Often, if you add another item to the container, a previous missing one will appear, but instead the new item disappears.
Storing items that you will not be using at equal to or less than 100% health will reduce the likelihood of items disappearing. Armor repaired to 125 can quickly fill up a container.
Note that if you are using mods which raise your maximum encumbrance the same glitch may also happen to your inventory.

Never heard of this. The only effects I've noticed is serious lag when opening a large inventory (hundreds of items with an encumbrance of 3,000+).

1. Have you broken out of jail? Quest items will not be in the evidence chest. You'll have to go to jail and serve time.

2. Any mods? A mod that removes the quest item flag means you could have easily sold it or dropped it someplace.

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I just remembered a glitch with containers doing something similar (if the player is technically a container); Items will seem to vanish from the container only to reappear when a significant number of other items are removed. From the wiki;

Hi and thanks for the reply

I haven't broken out of jail, if I ever stole something - by accident usually! - I pay the fine etc and the guards are leaving me alone. It sounds like it might be the over full inventory problem so I'll have to either store loads of things in a house or sell them etc, to see if it brings back the missing things, but if quest related items don't reappear I can't carry on with the quests which is frustrating. I have searched all through my inventory and the langourwine knife is definitely not showing even straight after I was given it I couldn't find it. I'll try it and see what happens

Note that if you are using mods TGM which raise your maximum encumbrance the same glitch may also happen to your inventory.