I detailed the updates made by the KoboTouch driver
earlier in the thread. I am using this most days on one or other of my four Kobos. I rarely see corrupted database.
Calibre also updates the metadata and cover in the book, but I doubt that is the problem.
But, disabling the driver and using "Save to disk" is probably the simplest way for a calibre user to get a lot of books to the device.