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I just tried with a non-DRM azw3 file. It seems to work OK. I used Tweak ebook on the azw3 afterward and opened the toc.ncx file in a text editor. The change was definitely there.
You did make sure it was the azw3 and not an epub for the same book that you viewed after the changes? Or is it feasible that the azw3 file is open somewhere and can't be re-written? I'm out of ideas.
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