That error is different. "OperationalError: unable to open database file" makes me think it is with the connection to the device. It sounds like it is being dropped or changed to readonly.
Something else to try is to see if Windows can still see the device and write to it between each calibre action. So, after calibre finishes its initial sync, check Windows can see it. Then try sending a book or deleting one and check again. And if you get an error like above, check again.
The other thing to try is another PC. Any chance of that?
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