Is there any way we can download the EPUB's and PDF's we'd uploaded to Apple books?
Certainly hope it's not locked into the Apple ecosystem.
Trying to download the pdf for use with logseq but couldn't find any option to download.
You could find books in /Users/<your username>/Library/Mobile Documents/iCloud~com~apple~iBooks/Documents
If you have storage optimization turned on then you will see only recently accessed books/files or whatever algorithm Apple uses deems necessary.
Making assumptions: 1) you are using a Mac, 2) the epub and pdf books are not DRM locked in any way.
Two methods:
PDFs only:
In Books, double clock the PDF. That opens it in Preview. You now use Save As... to save it wherever you want.
EPUBs and PDFs:
Make sure you have downloaded all the books you want by opening each one in Books.
In Terminal type:
open "/Users/user/Library/Mobile Documents/iCloud~com~apple~iBooks/Documents"
replacing user with your name and hit return.
This will open (in Finder) the iCloud Drive folder with all your downloaded books.
Now copy the books wherever you want. Don't move them.
Note: This may be macOS version dependent. I am using macOS 13.