I have a large ebook library which is stored on my PC in Calibre. I use the Calibre tag system to create collections within Calibre (on my Sony Touch these transferred over to the Sony without any extra work).
All I did with the Kindle was (using Calibre) sent one collection of books at a time, I then disconnected my Kindle from the PC, created the collection on the Kindle and added in those books, they disappear off the home page once you have added them to a collection. Then I reconnected my kindle to the PC and sent another collection
I now have 647 books on my Kindle in 46 collections. I took my about 3 hours.
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