Hi neil laubenthal,
Are these files stored locally on the Macs internal drive? After confirming the files are still in Finder, try importing them into Books again by selecting File > Import while in the Books app.
See more info here: Import books, audiobooks, or PDFs in Books on Mac - Apple Support (ME)
"Import books, audiobooks, or PDFs in Books on Mac
You can import content that you didn’t get from the Book Store or Audiobook Store, such as PDFs, mp3 audiobooks, Audible audiobooks, and many EPUB books.
Note: Some files (such as ACSM, AZW, and ODM) can only be opened in their associated third-party apps. If you’re not sure which app you need to open your book or audiobook, check with the library or eBook store that provided the content.
- In the Books app
on your Mac, choose File > Import. - In the Open dialog, select the books, audiobooks, or PDFs you want to import, then click Import.
- Note: You can also drag and drop books, PDFs, and some audiobooks into your library."
Let us know there results from there.
Cheers!