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It appears that you have a reasonably good understanding of the current situation.
Handwritten annotations made to a Print Replica book are stored as a Scribe notebook that contains only the handwritten content and none of the background of the book being annotated.
It is possible using the KFX Input calibre plugin to convert Scribe notebooks (including annotation notebooks) to EPUB format containing SVG images. The SVG images approximate how Amazon rasterizes the hand drawn strokes but do not match it exactly.
There are several options from there. The EPUB can be converted to PDF using calibre. The SVG can be extracted from the EPUB and then manipulated or converted to other image formats using an SVG editor such as Inkscape. Or you can import the SVG images into Microsoft Word or other software.
However there is currently no way to combine those annotations with the original PDF pages other than by using Amazon's services. Replicating that functionality is theoretically possible but would require a significant development effort to accomplish.
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