Yes, index referring file toc
I delete my ePub directly from iPad (select and delete)
And yes, I modify index (toc file), closed and reopening with calibre, see new index and them import to my iPad...but iPad use your memory for old index and not see new index!
With another prog, I go on file system of my iPad, I go into ebook folder, delete file toc of my ebook interest but after open my book on iPad and him see always old index!!
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