There is a copy in the internal database. It is an SQLite database and is in ".kobo/KoboReader.sqlite". The table of interest is called "Bookmark". Deleting all the rows in the table plus deleting the annotations files will remove all the annotations on the device.
A little bit better would be to set the value of the column "Hidden" to "true". When the book is next opened, the annotations will be removed from the file and the database. And if you are reading purchased kepubs, they will be deleted at the next sync.
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