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If you want to clean-up the shelves by directly editing the database, you can. But, as it is a dangerous thing to do, I will simply state the changes needed. If you understand them and want to risk it, go ahead. If you don't understand them, I recommend not attempting to do it.
The database on the device is an SQLite database. It is in ".kobo\KoboReader.sqlite". The shelves are stored in the "Shelf" table in the database. The columns to look at are "Name" and "_IsDeleted" and possibly one of the timestamps. Just deleting these rows is not enough. The next sync to Kobo will probably bring them back.
If you change "_IsDeleted" to "true" for all rows in the table, the shelves will be deleted from the device and the server at the next sync.
You can selectively change "_IsDeleted" to "true" for just the extra shelves. When I did this, I changed it for all duplicated shelves the except the one with oldest "CreationDate".
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