Typically when uploading ePubs into Books all that was required was to drag them either into the app directly or onto the Books icon.
In MacOS Sonoma Books accepts ePubs but rejects them about a minute or two later.
Curious about this behavior I went to the folder where ePubs are stored, and moved the books directly to it instead of via the Books app.
Once you move them into the folder, the same behavior that you see in the app happens with the folder (books appear in the folder, then vanish from the folder a minute or two later).
