I have had this happen a few times now. Getting the delete the book, instead of delete from device. These are all amazon books, some via library but still through amazon. Once in a while I get the popup on such books that its not going to get synced. All amazon books. A few times now I didn't even see the books in the cloud view on my Oasis, when they should be there of course. IN those cases I hit the sync button and they appeared.
In case of the non synced message or delete the book issue, I delete the book and then redownload back onto my device and then it says delete from device again as it should be.
Seems some glitching going on.
Haven't had any books go away though from my cloud/my account. At least I don't think so.
I don't even want that option on my kindle, the option to permanently deleting books. I don't want to be at the mercy of a touch screen for such important things.