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2Robocop
Check with MobiMetaEditor if that problem book has 113 exth record (ASIN). I'm sure 113 is missing. Missing ASIN causes books tagged for collection to appear in two places: In collection and in root even sorting view is set to Collection
You can perform an experiment: Download any epub book from our forum, convert it to mobi/azw3 using Calibre, add to any collection. Book will appear in collection only, not in the root.
Now delete this book from Kindle. Using MobiMetaEditor, open the book on PC and check exth 113. You'll see alphanumeric sequence (UUID) that Calibre placed as fake ASIN. Now delete exth 113 and copy "ASIN-less" file (will have suffix _new) to Kindle. Keep sorting to Collections, add book to any collection. Book will come up both in the collection and in the root.
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