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I use my Kindles and Amazon accounts together. However, I do have two Amazon accounts. One account strictly for my side-loaded books, and one associated with my main Amazon account associated with Kindle Unlimited, and Goodreads.
I purchase, rent, borrow, and download books from all over (the library, Smashwords, Goodreads, Author Websites, Amazon, Kindle Unlimited, Fan-fiction, Publisher websites....). Every single book I get goes into Calibre so I can side-load it into my Paperwhites in such a way that the series is listed before the title. No way can I use Amazon's standard way of listing the titles before the series, because there isn't room for both.
Because of this, I have a blank Amazon library that I don't purchase books from. This keeps the "cloud" from downloading a book and messing up my library.
I keep another two Kindles for my proper account and do not side-load anything (for the same reasons as above).
Interestingly enough, the Kindles still sync up with side-loaded books and collections.
Soooo...yes.
Calibre and Amazon are not mutually exclusive unless your sideloaded books get mixed up with your "in the cloud" books if you have them sent to your device in a way Amazon doesn't
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