I use Apple Books on an iPad Pro no problems. Multiple epubs from calibre and Apple Books store side-by-side.
Some questions:
- Is it Apple Books on an iOS/iPad device? (I think the app is also called Apple Books on Mac.)
- What do you mean by "visible"? Can you simply not see the book in Apple Books?
- Can you view the epub successfully in the calibre viewer? (This will eliminate DRM as an issue.)
- How did you add the book to Apple Books? (I have opened the book in OneDrive, sideloaded using iExplorer, or used the calibre content server.)