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It seems like you have imported the .mph-files. They keep bookmarks and highlights.
Did you import everything in the My Kindle Content-folder into calibre? You should just add the .asw-files.
Does your books show up in calibre? With proper titles and authors? The file size for these should be bigger than <0.1. If they do you can just delete the other files from calibre.
(If you want calibre to manage the bookmarks-files, you can add these to the corresponding books later)
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