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I believe you can't delete a category as long as there are any topics that exist in that category.
Have you made sure to delete all of the topics that are using the category?
However, before you do that, have you tried simply hiding them? From the top menu choose "Manage" and the the "Categories" button in the toolbar.
On every category page right beside the category name in the top line there is a check box labelled "Shown". If that box is unchecked, the category won't be shown as a choice any time you have to pick a category.
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