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Done a little more experimenting this morning and noticed that the problem appears to be that the kindle is not downloading popular highlights if a book is already on the device. It only downloads the highlghts file at the same time as the book is origially downloaded from the archive.
So if I download from archive, then move book+associated file to PC and then move just the book azw straight back to the device, the popular highlights are obviously missing, but the kindle makes no attempt to redownload them.
So it looks like calibre/conversion doesn't come into the equation at all. Just need to find out how to get popular highlights info redownloaded when a book has been loaded via usb rather than from the archive.
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