Some ePubs or PDFs are on your device, but do not appear in iMazing.
You are probably using iCloud Drive to synchronise the contents of the iBooks app. Unfortunately, documents and eBooks synced via iCloud Drive are not available to iMazing.
To disable iCloud Drive for iBooks on your device:
- iOS 10.3 or later: Settings > [your name] > iCloud > iBooks
- iOS 10.2 or earlier: Settings > iCloud > iBooks