never had this bug before, try loading the autosave when you entered the manor.
Display the Extra Books in actual Bookcases, not the Unique Books. I keep all the first copies of books My characters have collected in a single chest. I decorate Bookshelves by the Spines, and how the books stack. I do have Hjerim fully stocked and have not had books vanish, and Vlindrel Hall has not had any issues with My Necromancers.
I am careful about how many books I can place on an individual shelf, and watch how many I can place.
The Wolf Queen Series when placed on an eight book shelf will always have one of the volumes never sit correctly, it will always look crooked.
Always Save before decorating a Home, to avoid
Don't you have a manual save you can use to get them back?
As was said, the only thing you can do to avoid this in future is not put unique books (or any books you don't want to lose) on shelves. And save more often.
You on PC OP? Personally when the game bugs out on me i think it's ok to use a console command to add items back into your inventory.
There was this one time i had cleared a fort of bandits. I looted everything and i ended up being overburdened, so i started dropping stuff on the ground. One of the things i dropped was a stack of about 60 or so iron ore. But i didnt know that there was a bug, where if you tell your follower to pick up a stack like that the quantity gets changed to 1. So rather then saying ohh well game bugged out too bad, i did a console command and added back the 59 iron ore.
EDIT: and just to be clear i dont abuse the additem command to simply give myself gear or anything like that. I only do it when my inventory bugs out, which in about 300 hours of playtime has only happened twice.
Yeah, I'm not too good with saving all of the time. I just reverted back to no autosaves to speed up loading screens so I have to get used to it once again. The most recent save was prior to doing a bunch of smithing activities, enchanting, running back and forth to Falkreath to sell some stuff, etc. I wasn't willing to repeat the 30 minutes of mundane to save the books. I'll find them again I'm sure.
at the quantity gets changed to 1. So rather then saying ohh well game bugged out too bad, i did a console command and added back the 59 iron ore.
EDIT: and just to be clear i dont abuse the additem command to simply give myself gear or anything like that. I only do it when my inventory bugs out, which in about 300 hours of playtime has only happened twice.
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Xbox 360.
Yep. I'm going to move my valuable books now... and try to develop the save habit (because I really don't like autosave).