Happened to me early in the game and I haven't tried again since. In my case I put my pile of books inside a house right next to a fast travel spot. The next time I came back to add more books the whole loot bag was gone.
Some time later, I don't remember the specifics but that house and npc that lived there was involved in a quest . Maybe I had stupid luck and picked a particular house that has its contents reset or something.

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