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Originally Posted by Divingduck
Hm. This works for me fine since years. Had you check your global conversion template in preferences for format MOBI and AZW3 output options looks like? As BR wrote, the global template "defaults" will be overwritten from a manual changed template for a individual book. To reverse this behavior you need to set the preferences to default for these books.
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Thanks to a Windows update ("Destroyer's edition" or some such) which required a total reinstall, I lost my Calibre settings, which I had neglected to back up. I forgot to set the AZW3 output option after reinstalling, so everything since then was done using a ToC-at end. Then I changed the ToC-at-end setting, but still got ToCs at the end of some books, presumably those I'd converted previously.
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The only thing I am sometimes missing is a easy way to identify books with a non default individual conversion setups within the library. Maybe an enhancement for a plugin? 
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Absolutely. In desperation, what I ended up doing was bulk-converting all my books with ToC-at-end turned off to make sure this doesn't happen again. This took slightly over 3 days to run...
