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Yesterday Books began deleting all books in my library except for a proof generated by Books author, and four books purchased from the Apple store. I replaced the directories ~/Library/Containers/com.apple.iBooksX and com.apple.BKAgentService from backup to restore the library. Books deleted them again.

I upgraded to 10.14 from 10.12, and disabled syncing, the behavior persists.

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I had to give up and download my entire library from iCloud.

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