I'm guessing you did the setup using the Kobo desktop application rather than over WiFi. Or at least have used the Kobo desktop application with the Aura H2O. This has updated the internal database on the device past what is expected. But, if you read the full error message calibre displayed, there are instructions on what to do. While it is a warning, it is safe and will work. The instructions are to open the configuration of the KoboTouch driver, and select the option for "Attempt to support newer firmware". The next version of calibre will support this version of the database, but there are no problems with using the option.
Once you have the above, you can configure the the driver to do collection management.
https://wiki.mobileread.com/wiki/Kobo...nd_Collections is a good guide to do this.