If you set up a chiseled bookshelf with books in it using a command, when you try to add more books, the books you put in with the command disappear.

exsample:

/setblock -12 -61 8 minecraft:chiseled_bookshelf[facing=east,slot_0_occupied=true,slot_1_occupied=true,slot_2_occupied=true,slot_3_occupied=false,slot_4_occupied=false,slot_5_occupied=false]

In this case, there are books in the top shelf and no books in the bottom shelf. However, if you hold a book on the bottom shelf and right-click, everything on the top shelf will disappear and the book will be placed where you clicked.
The missing book will not remain in your inventory at this time.