Let the desktop app download and copy the the firmware update files to the device. Then remove the files and replace them with the files for the firmware you want to use.
The database also gets updated during this process and there is a possibility that it is incompatible. But, the changes Kobo makes are usually backwardly compatible to older firmware. The changes I can think of that are not, are in tables that pre 2.0.0 firmware didn't use.
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