Apple Books Collections Empty After macOS Mojave Update

Earlier today I updated to macOS Mojave version 10.14 from High Sierra. My university uses exclusively iBooks that they make (so nothing is purchased) to distribute courses content, so all of my material for school is stored in the Books app. Before the update, I had everything organized into collections based on class. Now, after the update, I know all of my books from school are accessible through the app, which I can see under the tab "List"

But, all of my collections are empty, except for this collection that I didn't create called "Books" that has all of the iBooks that used to be sorted into collections sorted into it.

Is there a reason all of my collections are empty? I really don't want to have to sort all of my 681 books back into their collections by hand.

Thank you.