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Just a thought.... If you updated your wife's Kobo with the original sqlite database from yours, did you set it up for her Kobo account before trying to sync it?
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Yes, I did. The cannot sync message was the same before and after I restored the database. My database hasn't been used or altered from new as I don't use it for books but only for personal data. Regardless, it made no difference.
I have the latest version of Calibre but that isn't an acceptable solution for my wife. It needs to work with the Kobo Desktop. I will have a look at the database to see if they are in there since it isn't encrypted.
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If you used the original version of the data base you may need to change the version in the database. It is likely that the new firmware will only read the database with the correct version.
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It reads the included books just fine.