Every weapon/book can be removed and placed back in the inventory by giving NPC a different weapon. Items that can't be retrived that way are: Troyan Horse, Dog Food, Moondrops, Demon Fan, Oden Can, Jade Necklace, Turtleshell Comb, Bear Figurine, and Genji Armor. You need first four of those items to recruit characters and the next five to fuck Lugia, Emilio, and Naonao.Not that I know of.
You should probably include this in the readme file, completionists will be happy that way.