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I do not mean to take the wind from your sails, but I think it is just a matter of weeks or months before Amazon's Send To Kindle service starts sending Print Replica (converted from PDF) to the Kindles they are still updating, which they are doing for Scribe and the Kindle apps. Unlike PDF, the annotations and reading position sync between devices, and you can export them directly (at least from the apps and Scribe).
The necessary PR support is already there: you can take a Print Replica document delivered to Scribe and side load it to another Kindle running recent firmware, and it renders and functions as expected (and even syncs!).
One thing that does not work well is export of the entire document to PDF (allowed currently only from Scribe). Scribe annotations are not converted to PDF annotations, and it also does not preserve hyperlinks and the ToC is not converted back to PDF bookmarks.
So there might be some interest in a tool in terms of taking annotations created for the Print Replica document and restoring them to the PDF it was converted from (on Scribe there are also pen annotations to consider).
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