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The two files you mentioned in the root of the exposed partition are calibre files and nothing to do with the Kobo database files. To restore a corrupted Kobo database, you would copy the KoboReader.sqlite and Bookreader.sqlite files into the .kobo directory. Since the Kobo ereader.conf is very likely to get reset as well, you would copy that file into the .kobo/Kobo directory. You would also loose the screensaver directory inside the .kobo directory.
I would again recommend doing a reboot before connecting to your computer. There have been several message threads which included the NickelMenu entries to do that.
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