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I'm having a similar issue. I can send books to my Kobo Glo and delete them just fine, but I cannot manage shelves. I've upgraded to the latest firmware and the latest version of Calibre, and I keep getting the same error:
calibre, version 2.6.0
ERROR: Error: Error communicating with device
disk I/O error
Traceback (most recent call last):
File "site-packages\calibre\gui2\device.py", line 87, in run
File "site-packages\calibre\gui2\device.py", line 532, in _sync_booklists
File "calibre_plugins.kobotouch_extended.device.driver" , line 337, in sync_booklists
File "site-packages\calibre\devices\kobo\driver.py", line 923, in sync_booklists
File "site-packages\calibre\devices\kobo\driver.py", line 2212, in update_device_database_collections
File "site-packages\calibre\devices\kobo\driver.py", line 2674, in check_for_bookshelf
File "site-packages\calibre\devices\kobo\driver.py", line 2584, in get_bookshelflist
OperationalError: disk I/O error
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