ibook issue on imac

Tried your steps to reset iBooks to esolve the "duplicate PDF files" issue under Sierra (per this OP iBooks, iCloud, Metadata mess - how do I reset database and start over?), but all books, purchases and PDFs, were still listed in iBooks after restart. The PDFs appeared instantaneously, so they were not downloaded from the real iCloud Drive (as opposed to the local copy in Containers, which was removed per your instructions).

Is there an updated method for resetting iBooks in Sierra?

FWIW, posted my own question on this topic here: How to reset iBooks to eliminate PDF duplicates?

Might be corrupted iBook preferences.

Open the Finder. From the Finder menu bar click Go > Go to Folder

Type or copy paste the following:

~/Library/Preferences/com.apple.ibooks.plist

Click Go then move the com.apple.ibooks.plist file from the Preferences folder to the Trash.

Restart your Mac then try opening an iBook.

Please read this whole message before doing anything.

Back up all data.

Quit iBooks if it's running. Test after taking each of the following steps that you haven't already taken. Stop when the problem is resolved. Quit iBooks again before going on to the next step.

Step 1

Hold down the option key and select Go ▹ Library from the Finder menu bar. From the Library folder, move the following item, if it exists, to the Trash:

Cookies/com.apple.ibooks.cookies

Step 2

Delete this item in the same way:

Preferences/com.apple.ibooks.plist

Step 3

Delete this item:

Containers/com.apple.iBooksX

and move this one to the Desktop:

Containers/com.apple.BKAgentService

Restart the computer. To log out and log back in is not enough—you must restart.

When you launch iBooks, you'll be prompted to reset the library. Confirm. The library will be empty. Rebuild it by downloading your purchases from the iBooks Store and importing any other content you added. You may find the added content in the folder named "com.apple.BKAgentService" that you moved to the Desktop.

do you think/know whether executing the steps you outline above will put paid to any highlights or annotations made in books not purchased from the iBooks store?

can you move com.apple.BKAgentService back