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The images in Digital Editions/Thumbnails seem to be created (by ADE) when you connect the device to ADE. I deleted the whole Thumbnails directory, and have had no problems.
The files in Digital Editions/Annotations and Digital Editions/Manifest are created by the device when you first open a book, and when you make annotations in the book, and remain there even after you delete the book. You can delete them too if you want. (The annotations are stored in the device's database too, but those ones are deleted when you delete the book.)
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