If you have any Print Replica books, they will not appear on Kindle.
I have Voyage, 5.9.5. The counts differ between it an iOS on 4 of the 7 collections I have, even taking PR books into consideration. 3 show higher count on Kindle, one higher on iOS. Manage Your Content and Devices is even more deviant, showing higher counts than either for 6 of the 7 collections.
So my conclusion is that there are problems everywhere, and not just on Kindle. But it will be a major research project to figure out what is wrong, much less to fix it.
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