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After disconnecting from the PC, the Reader should check through the file system and update the DB with information from the filesystem.
For the Sony Readers, the SQLite DB acts like the older XML caches. Useful for speeding up the device, but the filesystem is the final word. However, the trigger for a refresh is usually disconnecting the USB cable.
How did you delete these files? When I delete them directly from a PC it behaves correctly and removes them. Did you delete them from the device itself using a file explorer on the Reader?
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