The article that King_Penguin provided for you explains what you need to do to see books that are not purchased via the iBooks store on your iPad:
You can download ePub, iBooks Author books, and PDF files from iCloud Drive to your iPhone, iPad, iPod touch, or Mac.
- Open iBooks.
- Scroll to find the item that you want to download.
- Tap the Download icon in the upper-right corner of the item that you want to download. The item downloads to your library.
If you turn off iBooks in Settings > iCloud > iCloud Drive, iBooks items that you save to iCloud Drive will no longer be available on that device.
The last sentence is particularly important. You need to make sure that iBooks is turned on under iCloud Drive when you click on your name at the top of the Settings App, then on iCloud. Scroll down to the iCloud Drive section and make sure that iBooks is turned on.
Read the link that King_Penguin provided. Books that are not purchased from the iBooks store are not sync'd via iTunes. They must be sync'd using iCloud Drive.
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