Blue2,
I had a look at the code to see what is happening where you are seeing the errors. Calibre can't open the database on the Kobo Touch to remove the entries for the books you are deleting. But, it should have already opened the database when you connected the device. Which means that you should have gotten an error earlier.
As an experiment, could you try to get the annotations for a book? If you don't have annotations on any book, try it for a book you have started reading. This will add to the comments, how far through the book you are. The main thing this will tell us is if Calibre can read the database at all.
David
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