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There is no way that would ever have worked. The highlights are particular to one specific file, and so would not transfer from the original file to a new file that you create with corrections, etc.
The highlights should be in "My Clippings.txt", which will also have the location of the entry. It does not have the full text of the book with it. You can, if the original file does not have DRM, and it doesn't sound like it does, you can convert it to Word or HTML or whatever, edit it, and send the revised copy to your Kindle, either via USB, or via the Amazon email service. But the highlights will not appear in the revised file, since it is a new file, as far as the Kindle is concerned.
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