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I don’t use calibre for much so I don’t know anything about managing collections with it.
But if your collections are supposed to sync with Amazon, it can take some time before they reconstitute themselves. Once collections are more than a few hundred items, it can take a Kindle better part of a minute to add or remove items. And it seems the Kindle stops counting with collections of 1000 or thereabouts. All of this is fine if you read on tablets and phones, no performance issues whatsoever. I don’t really understand why Kindle has such a difficult time with large collections, but I suspect they just have not given it much attention, because 95% of Kindle users do not use them (my guess).
My advice would be to keep them smaller than a couple of hundred each.
But easy for me to say: my usage of collections is minimal and when the Read/Unread feature showed up, I was able to get rid of my two largest and problematic collections. I just have six now, the largest is less than 100 items, and I could probably get by with 3.
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