I know on the Kindle Touch if I change the title metadata with calibre and replace the (Amazon-purchased) book, if it was in a collection, the KT gets confused about whether it should be in the collection or not. I usually get around this by not putting anything into collections until I have set everything in calibre. IF I forget, I need to reload the original form of the book, with the lousy title including junk like ": A Novel" and delete it in that form from the collection. Then replace the book with a corrected title and proceed like normal.
Maybe this is the same problem?
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