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The best approach here is to use calibre and the Kobo Utiltiies plugin. In the Utilities select Database Fix Duplicate shelves. Make sure that the option to "Purge duplicate shelves" is not selected.
Once the unwanted shelves are gone, do a WiFi sync to the calibre cloud and let the purges flow upwards to the cloud.
I know you don't want to use calibre but trust me, try it for just this one case.
If you really want to make sure that nothing inadvertent happens, grab a copy of the KoboReader.sqlite file before doing the cleanup; in worse case you can put that file back afterwards.
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