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The persistent user store on /var/local may have a corrupted collections or document index database or something similar. You could try removing all content from the documents folder, reboot, add the files back, and reboot again. That "might" rebuild the indexes.
The device is not bricked. If it was mine, I would uninstall all hacks (reinstall first if necessary and then uninstall), then do factory reset. You can copy your books in later.
The kindles format and rebuild the persistent store and the usb drive if not they cannot be mounted due to corruption. To reformat the user store (usb drive) you can copy reformat it from the host pc, or on the kindle you need to loop mount the device to /mnt/mmc with an offset of 8192.
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