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Create Index will only create entries for words that are listed in the Index table or are marked for indexing in the HTML files. If the list is blank (and there are no words marked) then no words will be added to the index. And if you leave words in the list from one book to the next, you might index the wrong words.
However, if you want to index all the words in the EPUB just right-click on the Index list and select Autofill. This will load the list with every unique word found in the book ready for indexing.
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