The way books, especially those not purchased from the iBooks Store, sync across to all devices has changed with recent iterations of iTunes and iBooks. If you do not see all your files, including your PDFs, on all devices, confirm your preferences and settings are correct.
1a. On your Mac: System Preferences > iCloud > under the iCloud Drive heading > iBooks must be turned ON.
1b. iBooks > Preferences > General > Sync > Sync bookmarks, highlights and collections across devices should be checked.
2. On your device: Settings > your name > iCloud > iCloud Drive and iBooks must be ON.
3a. On your device, in iBooks app: tap on Collections at top center of screen (the name appearing there will vary depending on which Collection you’re browsing).
On iPad you’ll see a pull down menu appear. On iPhone you’ll see a new screen.
3b. At the bottom of the screen, ensure Hide iCloud Books is NOT selected.
4. All your iBooks files stored in iCloud Drive should now appear in iBooks on your device. To download the file to local storage, tap on the cloud icon.
Note: Instructions and illustrations are based on macOS 10.13 High Sierra and iOS 11.