I could swear I've done this in the past, but how escapes me. I would like to stop new books from reappearing in my bookshelves every time I put them in the inventory and then move to a new location. Is it possible?

If you have SP installed check the general option
Repopulate Empty Library Shelves
When enabled, empty library shelves are restocked with their appropriate book type
Default: True
Module: Extra StoryProgression

Maybe this can stop the restocking - set it to False.

Could be mistaken, but doesn't that setting only apply to bookshelves that are on lots that are actual Libraries?

You may be right, it was just a suggestion.
I think the general stocking bookshelf is system related and can be adjusted at least easily with Retuner


Sims3.Gameplay.Objects.ShelvesStorage.Mimics.BookShelfFuture,Sims3GameplayObjects
kBookshelfTuning
NumStartingBooks
<Value>5</Value>

Sims3.Gameplay.Objects.ShelvesStorage.Mimics.BookShelfFuture,Sims3GameplayObjects
kBookshelfTuning
StartBookMaxValue
<Value>150</Value>

So if tuning these ones the restocking can be reduced or even stoped I guess.
If you wanna stock a special shelf use Debugenabler

click the shelf and use
Add Fishing Books (only; Bookshelves)
Add Skill Books (only; Bookshelves)
Add Toddler Books (only; Bookshelves)
Stock with Genre

and maybe you need to do it for each differnt bookhelfs, or use only one type, because there are a lot

To get the name of the bookshelf use Debugenabler, click the bookshelf and use
Name of type (or similiar expression)