In addition to taming's suggestion...
You could contact customer support. I tried this, but they wanted me to create a new account, so I declined their help.
If you are comfortable with a PC and databases, you can edit the database on the kobo. I did this, and I was able to delete the shelves (and duplicates). However, the next time I synced, the shelves came back (but there were no duplicates).
If
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