I have two EPUB books downloaded from a non-Apple website.
If I open Apple Books on my Mac and try to delete/remove the first of them, the app asks me whether I want to remove it from my “Reading Now” collection:
But if I try to delete/remove the second one, Books asks me whether I want to delete that book from the device. Why? (And by the way, no, it doesn’t delete the file if I answer “Delete”. Why?)
Ventura 13.2.1, Books 5.1
Reading Now is a special collection that is automatically maintained by books you’ve opened and read some portion of (just opening & closing the book isn’t enough, you have to turn some pages). It looks like the second one isn’t one you are “Reading Now”.
Removing something from “Reading Now” doesn’t delete it from your device, it just doesn’t show up in that collection any more. For example, I often will open up a book as reference and it’ll end up in “Reading Now”, but I remove it from again, because it’s not one of the books I’m reading, just one I looked something up in. This is more understandable when you have a lot of books installed, and you want your “Reading Now” to be the books you’re currently interested in. “Deleting”, on the other hand, either means removing the download or deleting it from your library entirely. My version isn’t giving the same dialog you’re seeing, but I’m guessing you’d get the same choices if you clicked “Delete”. Maybe install a free book from Gutenberg.org and test it if you’re not sure.