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Unreferenced images are deleted, which you will see if you look at the conversion log. And no, there is no way to do a conversion and just add a ToC.
Conversion *will* alter your file. Though if I was you, I'd stop worrying about the changes conversion is doing to your file, there are more important things to worry about in life.
And just for completeness if your file was in a modern ebook format like epub of azw3, you could use the edit toc tool to "just" add a table of contents.
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