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When you connect the Kobo to your computer, the "root" folder displayed for the device is actually the /mnt/onboard/ directory on the Kobo's file system. (Devices with SD card may also have /mnt/sdcard/ or similar.)
If you move books outside the KOReader file browser, to retain the book settings and other book metadata you need to move the *.sdr folders along with the book files. (By default, they are located in the same folders as the books.) Those folders are not visible in the KOReader file browser, but will be automatically moved to the correct location if moving books within there.
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