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I have the following devices: iPhone, iPad Pro, MacBook Air and a 27" iMac. All devices have the most current OS installed. My iBook documents all sync together except for the ones on the iMac. I just can't figure out why. I am signed into iCloud and everything is checked that needs syncing.
MacBook Air, macOS Sierra (10.12.3)
I am having the same problem on my Mac (10.13.2). And I could not solve it.
I had this problem too and was puzzled by it but managed to find the solution:
What you need to do is go to the device where files are not being syncronized and go to Settings>iCloud and then switch off iCloud, wait a moment, then switch it on again. If this doesn't work then do the same for the iBook switch under the iCould settings. Once you switch both back on again, it will refresh and all your saved files will be restored. Hope that helps!
I was able to sync my iBooks by going to my Mac system preferences and choosing icloud, icloud Drive options and check off iBooks under (Apps that store documents and data in icloud will appear hear). I hope this helps for anyone that has this issue too.
EDIT: I missed a setting on my iPhone to synch, apparently I didn't have iBooks toggled in iCloud settings (which is harder to find now - I sure wish that they didn't keep moving settings around - Oh well, problem solved).
Thank you. I had the same issue and found that, for I don't know what reason, iBooks was unchecked under iCloud Drive options...
This also fixed it for me... iBooks was unchecked on my Mac under System Preferences > iCloud > iCloud Drive Options
iBooks on my Mac are not syncing
