Thank you for your help ixtab. I did what you said and it's now working again, collections and everything.
I have an idea what might have caused it. When I was in CM I turned on "Display collections only". I assumed that was only for display in CM, but maybe that somehow turned standard for the entire Kindle? I could see the collections, just not any books.
I couldn't get into CM after the books were gone so I couldn't try to turn it off again. Maybe I'm just rambling, but maybe it is worth checking out. I'm staying away from that option from now just in case and hopefully it will work fine now.