All spells are listed in Scripts/Spells/Initializer.cs. Each one requires a unique number. Group them together by spellbook. This is where you change the order of spells, place them in other groups to move them around, or just delete ones you don't want. Make sure the spells are numbered in order without skipping numbers within a book. You must delete existing spellbooks of that type on your server first! Failure to do that will crash the server if you open one of the older books in-game.
Looking at Items/Equipment/Spellbooks/NecromancerSpellbook.cs you'll see the spells are defined with "offset" =100 (start at spell 100) and "count" = 16 or 17 (depending on era) so that fills the book with spells 100-117 as necessary. Adjust the count for each book as required to match the number of spells you will have within it.
All reagents for any kind of spells must be listed in Scripts/Spells/Reagent.cs
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Oops - I may have over-thought my reply. If you want to do that in-game, the short answer is "it's probably not worth the PITA of coding it." There's not a method within the game to drop a spell from a book (no button like a runebook).
Each spellbook has a "Content" value that lets it determine what spells are within it. You'd have to do the math to figure out the book's new value after removing a spell, and that's after providing a method by which to pick a spell for removal.