"The operation couldn’t be completed. (BKAgentServiceErrorDomain error 8.)"
This is crazy, but it worked (after everything else failed). I opened:

~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Updates


And clicked on the ePub/PDF files there. iBooks opened them. In my case, I had 1 ePub file, and 1 PDF file. I don't know how or why, but I can confirm that it is an issue related to the Updates folder, because simply deleting that folder caused the problem to resurface.

To all those out there - good luck dealing with this infuriating app.