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You should definitely delete problem books from the documents folder before sending new books. You can use calibre to delete the books if you want.
There is no benefit in doing the conversion more than once. Either a conversion fixes the problem or it does not.
And note that the indexer basically scans the files on the kindle in some fixed order so any new files that are after the problem book in that order, will not show up because the indexer stops before getting to them. If a new file is before the problem book it will show up.
The key is to identify the problem book and try reconverting it and sending it.
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