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After syncing books moved from collections to Books section constantly. Is there a fix for this?

I have an iPhone 6 Plus and an iPad Mini first generation.

Both are the newest system as well as my Macbook Pro running El Capitan.

When I sync my iBooks in both devices, I am left with random books taken out of my different collections into Books. I have to manually place them back into its Collections every day. Its super annoying and its never the same books.

This also happens not just on my Mac's iBooks but all my iDevices too.

Is there a fix for this? Can anyone share if they know how to resolve this issue?