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That error has absolutely nothing to do with where the calibre database and directory are. In fact, it has nothing to do with calibre except that it was run by a plugin in calibre.
You are using the Kobo Utilities plugin to do a backup of the database that is on the Kobo device. What this does is copy the database file from the device to a directory that you configure in the plugin. After the copy has been done, the plugin checks the database is valid. In this case, that failed.
What this usually means is that the database on the device is corrupt in some way. Exactly what will happen depends on how bad the problem is and were it is. Frequently, if you get the error during the backup, then you will also get an error when calibre access the database to get the list of books. But, the check is for all of the database and the problem could be in an area that is not access by calibre.
With a corrupt database, usually what happens is that if you restart the device, you will notice the problems. For a lot of things, the device runs on in memory copies of the data and writes to the database as needed. And only reads when the device is started or when some of the less common functions are done. That means that if you restart, you might lose the reading status or collections or books might need to be reimported.
There is a possibility that the corruption was caused during the copy. So, I suggest checking the database on the device. There is a function in the Kobo Utilities plugin to do this. If there are errors, then it should be OK and hopefully it is a once-off copy problem. If there are errors, you will need to fix it. Either restore a recent database backup, and restart the device as soon as you remove it from the PC. Or signout from the Kobo account on the device. When you signin again, a new database will be created. But, you will lose reading status for sideloaded books.
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