Sounds like your reader is failing. You can still transfer books to it using save to disk in calibre, but if calibre cannot read the db file, then it cannot connect to it as a device.
You can also disable the sony driver interface plugin in preferences->plugins and connect to the reader using connect to folder in calibre, which is a bit more convenient than save to disk.
However, since your reader is failing, it's likely other things will break soon.
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