I also use calibre to organize my books. I only use Kindle collections for unread/read categorization and I only keep a dozen or so unread books on my devices. I am always near wi-fi so adding more books from my Amazon account is easy anytime.
I have seen hints that Amazon will soon allow the ability to filter books by read/unread, automatically marking books as read once they are completed. (I believe that Kobo already has a feature like that.) That may eliminate my need for collections entirely.
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