Some of Apple's cloud processes can be really difficult to fix when they break. A year or so ago, I had an issue with Apple Music. Basically, I all of a sudden started to get weird recommendations for styles of music I never listen to. My guess is somewhere, somehow, my account go confused with someone else's account. It took a lot of calls and back and forth's before if finally started working again.
I stopped trying to put my non Apple purchased books in iCloud. At the time I tried it, it seemed that iCloud didn't handle a large number of books well. They don't seem to have the same issue with Music or Movies.
I use Calbre Companion to hold my books, then transfer them to the reading app for reading, then delete from the reading app when I've read them. Thus, I've never bothered trying to put my books back in iCloud after that first try several years ago.
For the most part, both Kindle and Books seem to be designed for people who have small libraries and only keep a handful of books on the device at a time. Both slow down significantly with lots of books and neither really have the tools that are available with Calibre that allows me to manage my library.
Some aspects of the new Books are interesting, for example, Books will give you all sorts of information for books you purchased from Apple, i.e. is it part of a series, if so what are the other books in the series. Unfortunately, that sort of stuff seems to work only for Apple books.
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