Just upgraded from iPhone 4s to 6 +. All my PDF files in iBooks migrated ok. The purchased books did not. When I first opened iBooks on the 6+ the book icons were there but statement: "not on this device" appeared. When I tried to fix by clicking on the "looping arrow" icon, the book icons then disappeared.
The books are still in the MacBook iBook library and open fine. What to do?