Add only one collection of books to the Kindle.
Eject
Add all the most recent books to new or desired collection.
Don't sync as it can mess up Collections.
You need a registered Kindle to create Collections.
Obviously most people manually add new titles to Collections manually on Calibre and may often edit the Tag metadata as it's often nuts.
I prefer managing collections on Calibre and using the Kobos. More than a hundred books is a pain to manage on every make / firmware of ereader or android app I've ever used. The developers should be made to use a professional library/document management system and sort 2,000+ books on an eReader that are randomly added.
They should implement nested categories/collections and have a file/collection manager too. All the standard book categories should exist. Tags should NOT automatically create Collections (Sony madness), but be searchable too.
Management and search on EVERY ebook reader/app apart from Calibre is a disaster. It's obnoxious of Amazon that they removed ability of various user settings, have a large minimum margin and crippled Collection management to really be only via a registered Kindle and your Amazon Account device settings on the Web.
NO ereader should depend on the Internet or a server for functionality. A stupidity also on some BluRay discs.
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