If you go to place books on a shelf that already has them, some of the books that are already on there will just disappear.

I don't know the cause, perhaps it was from moving the books around while already on the shelf, I don't know, but who knows how many books I have already lost to this without noticing.

Does this affect the bookshelf in the main hall, or the ones in the library wing, or both?

I have this problem with shelves in my other houses. Been around since before Dawnguard

This has been around since the 1.4 patch cluster****. It was supposed to have been fixed.

Cannot say I have ever noticed it, but then I have only ever put my spare books on the shelves, the main collection stays in storage. I often check if the shelves are full and have never lost any books. No I have never tried to add more books to a full bookshelf, will test it out later. My current character has plenty of books.

i only have that problem with hearthfire

and the one in the basemant in riften

all the other shelves are fine