Books on Apple Books are missing

I download PDFs of books or articles online and I like reading them on Apple Books since I can highlight things and add annotations that are saved to both my laptop and phone. Today I tried opening a book and noticed that all of my books and PDFs were gone. I looked at the original downloaded PDFs in my files and all of the highlights and annotations are gone. I am doing research so this is very inconvenient, I cant just lose all that work. What happened and how can I get the highlights back?